From 0e89124a13cb8a95db4d74fdc9e6780d7abc0e6e Mon Sep 17 00:00:00 2001
From: galaxybot <galaxybot@users.noreply.github.com>
Date: Sat, 27 Apr 2024 03:26:22 +0000
Subject: [PATCH 1/3] Update Python dependencies

---
 lib/galaxy/dependencies/dev-requirements.txt     | 16 ++++++++--------
 .../dependencies/pinned-lint-requirements.txt    |  4 ++--
 lib/galaxy/dependencies/pinned-requirements.txt  |  8 ++++----
 .../pinned-typecheck-requirements.txt            |  4 ++--
 4 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index f963631db7b0..59178ed6dc9d 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -9,7 +9,7 @@ axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.13"
 babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
 backports-tarfile==1.1.1 ; python_version >= "3.8" and python_version < "3.12"
 backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
-black==24.4.0 ; python_version >= "3.8" and python_version < "3.13"
+black==24.4.2 ; python_version >= "3.8" and python_version < "3.13"
 build==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -19,9 +19,9 @@ click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
 codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
 contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
-coverage[toml]==7.4.4 ; python_version >= "3.8" and python_version < "3.13"
+coverage[toml]==7.5.0 ; python_version >= "3.8" and python_version < "3.13"
 cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13"
-cwltest==2.5.20240304113812 ; python_version >= "3.8" and python_version < "3.13"
+cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
 darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
 darkgraylib==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -56,7 +56,7 @@ jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
 jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "3.13"
 jsonschema==4.20.0 ; python_version >= "3.9" and python_version < "3.13"
 junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
-keyring==25.1.0 ; python_version >= "3.8" and python_version < "3.13"
+keyring==25.2.0 ; python_version >= "3.8" and python_version < "3.13"
 kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13"
 lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
 markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -83,7 +83,7 @@ pbr==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
-platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
+platformdirs==4.2.1 ; python_version >= "3.8" and python_version < "3.13"
 playwright==1.43.0 ; python_version >= "3.8" and python_version < "3.13"
 pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -119,7 +119,7 @@ pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
 readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13"
-referencing==0.34.0 ; python_version >= "3.9" and python_version < "3.13"
+referencing==0.35.0 ; python_version >= "3.9" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
 responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -133,7 +133,7 @@ schema-salad==8.5.20240410123758 ; python_version >= "3.8" and python_version <
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
 scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
-selenium==4.19.0 ; python_version >= "3.8" and python_version < "3.13"
+selenium==4.20.0 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
 setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -160,7 +160,7 @@ tomli==2.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0a6"
 trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
 trio==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-twill==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
+twill==3.2.4 ; python_version >= "3.8" and python_version < "3.13"
 twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
 typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index fea2eeeb9fa8..951a6bf4792f 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -1,7 +1,7 @@
 attrs==23.2.0
 flake8==7.0.0
-flake8-bugbear==24.4.21
+flake8-bugbear==24.4.26
 mccabe==0.7.0
 pycodestyle==2.11.1
 pyflakes==3.2.0
-ruff==0.4.1
+ruff==0.4.2
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 37b51a528176..007384ec0854 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -122,7 +122,7 @@ oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
 paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
 parsley==1.3 ; python_version >= "3.8" and python_version < "3.13"
-paste==3.9.0 ; python_version >= "3.8" and python_version < "3.13"
+paste==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
 pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -148,7 +148,7 @@ pylibmagic==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
 pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13"
 pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.13"
-pysam==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
+pysam==0.22.1 ; python_version >= "3.8" and python_version < "3.13"
 python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13"
 python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13"
 python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13"
@@ -157,7 +157,7 @@ pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13"
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
 pyzmq==26.0.2 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
-referencing==0.34.0 ; python_version >= "3.8" and python_version < "3.13"
+referencing==0.35.0 ; python_version >= "3.8" and python_version < "3.13"
 refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13"
 regex==2024.4.16 ; python_version >= "3.8" and python_version < "3.13"
 repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
@@ -178,7 +178,7 @@ setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
 shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
-social-auth-core==4.5.3 ; python_version >= "3.8" and python_version < "3.13"
+social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
 sqlalchemy==2.0.29 ; python_version >= "3.8" and python_version < "3.13"
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index 014e6a3a3cb5..99e1264d74fd 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -3,7 +3,7 @@ cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_
 cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13"
 lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-mypy==1.9.0 ; python_version >= "3.8" and python_version < "3.13"
+mypy==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
 pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
 pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -20,6 +20,6 @@ types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
 types-python-dateutil==2.9.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
 types-pyyaml==6.0.12.20240311 ; python_version >= "3.8" and python_version < "3.13"
 types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
-types-six==1.16.21.20240311 ; python_version >= "3.8" and python_version < "3.13"
+types-six==1.16.21.20240425 ; python_version >= "3.8" and python_version < "3.13"
 types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13"
 typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"

From 0629908541043d93063df8832c8f94d6d41bb3ca Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sat, 27 Apr 2024 16:03:22 +0100
Subject: [PATCH 2/3] Fix new UP031 errors from ruff 0.4.2

---
 .../webhooks/demo/tour_generator/__init__.py  | 28 ++++-----
 doc/parse_gx_xsd.py                           | 32 +++++-----
 lib/galaxy/actions/library.py                 |  2 +-
 lib/galaxy/auth/providers/ldap_ad.py          |  4 +-
 lib/galaxy/config/__init__.py                 |  5 +-
 lib/galaxy/datatypes/binary.py                | 14 ++---
 .../interval_to_bedstrict_converter.py        |  2 +-
 .../converters/maf_to_fasta_converter.py      | 11 ++--
 .../converters/wiggle_to_simple_converter.py  |  2 +-
 lib/galaxy/datatypes/interval.py              |  6 +-
 lib/galaxy/datatypes/neo4j.py                 |  3 +-
 lib/galaxy/datatypes/proteomics.py            |  2 +-
 lib/galaxy/datatypes/qiime2.py                |  4 +-
 lib/galaxy/datatypes/registry.py              |  5 +-
 lib/galaxy/datatypes/tabular.py               |  2 +-
 lib/galaxy/datatypes/tracks.py                |  3 +-
 lib/galaxy/datatypes/xml.py                   |  2 +-
 lib/galaxy/job_execution/actions/post.py      |  4 +-
 lib/galaxy/jobs/__init__.py                   |  3 +-
 lib/galaxy/jobs/runners/__init__.py           |  2 +-
 lib/galaxy/jobs/runners/aws.py                |  2 +-
 lib/galaxy/jobs/runners/pbs.py                |  4 +-
 .../jobs/runners/state_handlers/resubmit.py   |  4 +-
 lib/galaxy/jobs/runners/util/cli/job/lsf.py   |  2 +-
 lib/galaxy/jobs/runners/util/pykube_util.py   |  2 +-
 lib/galaxy/managers/interactivetool.py        |  9 +--
 lib/galaxy/managers/markdown_parse.py         |  4 +-
 lib/galaxy/managers/markdown_util.py          | 10 +--
 lib/galaxy/managers/users.py                  |  2 +-
 lib/galaxy/model/__init__.py                  |  7 +--
 lib/galaxy/model/deferred.py                  |  4 +-
 lib/galaxy/model/store/__init__.py            |  2 +-
 lib/galaxy/objectstore/__init__.py            |  4 +-
 lib/galaxy/objectstore/rucio_extra_clients.py | 14 ++---
 lib/galaxy/selenium/sizzle.py                 | 13 ++--
 lib/galaxy/tool_shed/tools/tool_validator.py  |  7 +--
 lib/galaxy/tool_shed/util/shed_util_common.py |  2 +-
 lib/galaxy/tool_util/deps/brew_exts.py        |  4 +-
 .../tool_util/deps/mulled/mulled_build.py     |  2 +-
 lib/galaxy/tool_util/parser/xml.py            |  3 +-
 lib/galaxy/tools/__init__.py                  |  6 +-
 .../tools/error_reports/plugins/gitlab.py     |  2 +-
 lib/galaxy/util/markdown.py                   |  2 +-
 lib/galaxy/util/topsort.py                    |  2 +-
 .../web/framework/middleware/profile.py       |  2 +-
 lib/galaxy/webapps/base/webapp.py             |  2 +-
 .../webapps/galaxy/controllers/admin.py       |  6 +-
 .../webapps/galaxy/controllers/dataset.py     |  2 +-
 .../webapps/galaxy/controllers/history.py     |  8 +--
 lib/galaxy/webapps/galaxy/controllers/page.py |  4 +-
 .../webapps/galaxy/controllers/tool_runner.py |  4 +-
 .../galaxy/controllers/visualization.py       |  2 +-
 lib/galaxy/workflow/modules.py                |  4 +-
 lib/galaxy/workflow/refactor/execute.py       |  4 +-
 lib/galaxy_test/api/test_libraries.py         |  2 +-
 .../dependencies/attribute_handlers.py        |  4 +-
 .../metadata/repository_metadata_manager.py   |  6 +-
 lib/tool_shed/repository_types/util.py        | 22 +++----
 lib/tool_shed/test/base/twilltestcase.py      | 10 ++-
 ...st_0440_deleting_dependency_definitions.py | 44 +++++++------
 lib/tool_shed/util/shed_util_common.py        | 10 +--
 lib/tool_shed/webapp/controllers/user.py      | 13 ++--
 scripts/api/common.py                         | 10 +--
 scripts/api/data_manager_example_execute.py   |  4 +-
 scripts/api/display.py                        |  2 +-
 scripts/api/example_watch_folder.py           |  8 +--
 .../filter_failed_datasets_from_collection.py |  3 +-
 scripts/api/history_create_history.py         |  2 +-
 scripts/api/history_delete_history.py         |  2 +-
 .../api/import_library_dataset_to_history.py  |  2 +-
 scripts/api/library_create_folder.py          |  2 +-
 scripts/api/library_create_library.py         |  2 +-
 scripts/api/library_upload_from_import_dir.py |  2 +-
 scripts/api/load_data_with_metadata.py        |  4 +-
 ...eset_metadata_on_installed_repositories.py |  2 +-
 scripts/api/workflow_delete.py                |  2 +-
 scripts/api/workflow_execute.py               |  2 +-
 scripts/api/workflow_execute_parameters.py    |  2 +-
 scripts/api/workflow_import.py                |  4 +-
 .../api/workflow_import_from_file_rpark.py    |  2 +-
 scripts/apply_tags.py                         |  6 +-
 scripts/build_toolbox.py                      |  2 +-
 scripts/check_python.py                       |  7 ++-
 .../admin_cleanup_datasets.py                 | 10 +--
 scripts/cleanup_datasets/pgcleanup.py         | 18 +++---
 scripts/config_sample_to_kwalify.py           |  8 +--
 scripts/db_shell.py                           |  6 +-
 scripts/drmaa_external_killer.py              |  2 +-
 scripts/drmaa_external_runner.py              |  6 +-
 scripts/dump_library_paths.py                 |  4 +-
 scripts/external_chown_script.py              |  6 +-
 scripts/grt/export.py                         |  2 +-
 scripts/loc_files/create_all_fasta_loc.py     | 61 ++++++++-----------
 scripts/microbes/create_bacteria_loc_file.py  | 14 ++---
 scripts/microbes/create_nib_seq_loc_file.py   |  4 +-
 scripts/microbes/harvest_bacteria.py          | 36 +++++------
 scripts/pages_identifier_conversion.py        |  4 +-
 scripts/runtime_stats.py                      | 24 ++++----
 scripts/set_user_disk_usage.py                |  4 +-
 scripts/tests_markdown.py                     |  4 +-
 scripts/tool_shed/api/common.py               |  6 +-
 scripts/tool_shed/api/create_categories.py    |  4 +-
 scripts/tool_shed/api/create_users.py         |  6 +-
 ...deprecate_repositories_without_metadata.py |  8 +--
 scripts/tools/re_escape_output.py             |  2 +-
 scripts/update_shed_config_path.py            |  4 +-
 .../chained_dyndest_rules/module2/rules.py    |  2 +-
 .../chained_dyndest_rules/module3/rules.py    |  2 +-
 .../integration/test_repository_operations.py |  4 +-
 test/integration/test_structured_dataset.py   | 10 +--
 .../gen_history_export_test_artifacts.py      |  2 +-
 test/manual/workflows_scaling.py              |  6 +-
 test/unit/app/queue_worker/conftest.py        |  2 +-
 test/unit/app/test_markdown_validate.py       |  2 +-
 test/unit/app/tools/conftest.py               |  2 +-
 test/unit/app/tools/test_wrappers.py          | 13 ++--
 test/unit/config/test_path_resolves_to.py     |  6 +-
 test/unit/data/test_model_copy.py             |  4 +-
 test/unit/data/test_quota.py                  |  2 +-
 test/unit/files/test_posix.py                 |  2 +-
 test/unit/objectstore/test_objectstore.py     |  2 +-
 test/unit/tool_shed/test_shed_index.py        |  2 +-
 .../unit/tool_util/mulled/test_mulled_list.py |  4 +-
 test/unit/tool_util/test_tool_deps.py         | 16 +++--
 test/unit/util/test_lazy_process.py           |  2 +-
 test/unit/util/test_rule_utils.py             |  4 +-
 test/unit/util/test_sqlite_utils.py           |  4 +-
 127 files changed, 381 insertions(+), 425 deletions(-)

diff --git a/config/plugins/webhooks/demo/tour_generator/__init__.py b/config/plugins/webhooks/demo/tour_generator/__init__.py
index 16219c91b402..3e5e39bb1d18 100644
--- a/config/plugins/webhooks/demo/tour_generator/__init__.py
+++ b/config/plugins/webhooks/demo/tour_generator/__init__.py
@@ -59,7 +59,7 @@ def _upload_test_data(self):
                 filename = test_datasets[input_name]
                 input_path = self._tool.test_data_path(filename)
                 if not input_path:
-                    raise ValueError('Test dataset "%s" doesn\'t exist.' % input_name)
+                    raise ValueError(f'Test dataset "{input_name}" doesn\'t exist.')
                 upload_tool = self._trans.app.toolbox.get_tool("upload1")
                 filename = os.path.basename(input_path)
                 with open(input_path, "rb") as f:
@@ -92,12 +92,12 @@ def _upload_test_data(self):
 
     def _generate_tour(self):
         """Generate a tour."""
-        tour_name = self._tool.name + " Tour"
+        tour_name = f"{self._tool.name} Tour"
         test_inputs = self._test.inputs.keys()
         steps = [
             {
                 "title": tour_name,
-                "content": "This short tour will guide you through the <b>" + self._tool.name + "</b> tool.",
+                "content": f"This short tour will guide you through the <b>{self._tool.name}</b> tool.",
                 "orphan": True,
             }
         ]
@@ -107,26 +107,26 @@ def _generate_tour(self):
                 continue
             step = {
                 "title": input.label,
-                "element": "[id='form-element-%s']" % name,
+                "element": f"[id='form-element-{name}']",
                 "placement": "right",
                 "content": "",
             }
             if input.type == "text":
                 if name in test_inputs:
                     param = self._test.inputs[name]
-                    step["content"] = "Enter value(s): <b>%s</b>" % param
+                    step["content"] = f"Enter value(s): <b>{param}</b>"
                 else:
                     step["content"] = "Enter a value"
             elif input.type == "integer" or input.type == "float":
                 if name in test_inputs:
                     num_param = self._test.inputs[name][0]
-                    step["content"] = "Enter number: <b>%s</b>" % num_param
+                    step["content"] = f"Enter number: <b>{num_param}</b>"
                 else:
                     step["content"] = "Enter a number"
             elif input.type == "boolean":
                 if name in test_inputs:
                     choice = "Yes" if self._test.inputs[name][0] is True else "No"
-                    step["content"] = "Choose <b>%s</b>" % choice
+                    step["content"] = f"Choose <b>{choice}</b>"
                 else:
                     step["content"] = "Choose Yes/No"
             elif input.type == "select":
@@ -138,7 +138,7 @@ def _generate_tour(self):
                                 params.append(option[0])
                 if params:
                     select_param = ", ".join(params)
-                    step["content"] = "Select parameter(s): <b>%s</b>" % select_param
+                    step["content"] = f"Select parameter(s): <b>{select_param}</b>"
                 else:
                     step["content"] = "Select a parameter"
             elif input.type == "data":
@@ -151,7 +151,7 @@ def _generate_tour(self):
             elif input.type == "conditional":
                 param_id = f"{input.name}|{input.test_param.name}"
                 step["title"] = input.test_param.label
-                step["element"] = "[id='form-element-%s']" % param_id
+                step["element"] = f"[id='form-element-{param_id}']"
                 params = []
                 if param_id in self._test.inputs.keys():
                     for option in input.test_param.static_options:
@@ -173,24 +173,24 @@ def _generate_tour(self):
                                 step_msg = f"Select dataset: <b>{hid}: {dataset}</b>"
                             else:
                                 case_params = ", ".join(self._test.inputs[tour_id])
-                                step_msg = "Select parameter(s): " + "<b>%s</b>" % case_params
+                                step_msg = f"Select parameter(s): <b>{case_params}</b>"
                             cond_case_steps.append(
                                 {
                                     "title": case_title,
-                                    "element": "[id='form-element-%s']" % tour_id,
+                                    "element": f"[id='form-element-{tour_id}']",
                                     "placement": "right",
                                     "content": step_msg,
                                 }
                             )
                 if params:
                     cond_param = ", ".join(params)
-                    step["content"] = "Select parameter(s): <b>%s</b>" % cond_param
+                    step["content"] = f"Select parameter(s): <b>{cond_param}</b>"
                 else:
                     step["content"] = "Select a parameter"
             elif input.type == "data_column":
                 if name in test_inputs:
                     column_param = self._test.inputs[name][0]
-                    step["content"] = "Select <b>Column: %s</b>" % column_param
+                    step["content"] = f"Select <b>Column: {column_param}</b>"
                 else:
                     step["content"] = "Select a column"
             else:
@@ -210,7 +210,7 @@ def _generate_tour(self):
         self._tour = {
             "title_default": tour_name,
             "name": tour_name,
-            "description": self._tool.name + " " + self._tool.description,
+            "description": f"{self._tool.name} {self._tool.description}",
             "steps": steps,
         }
 
diff --git a/doc/parse_gx_xsd.py b/doc/parse_gx_xsd.py
index d1453f86870b..e34a9ba89afd 100644
--- a/doc/parse_gx_xsd.py
+++ b/doc/parse_gx_xsd.py
@@ -34,7 +34,7 @@ def main():
 
 
 class Tag:
-    def __init__(self, line):
+    def __init__(self, line: str):
         assert line.startswith("$tag:")
         line_parts = line.split(" ")
         first_part = line_parts[0]
@@ -52,12 +52,12 @@ def __init__(self, line):
 
     @property
     def _pretty_title(self):
-        return " > ".join("``%s``" % p for p in self.title.split("|"))
+        return " > ".join(f"``{p}``" for p in self.title.split("|"))
 
     def build_help(self):
         tag = xmlschema_doc.find(self.xpath)
         if tag is None:
-            raise Exception("Could not find xpath for %s" % self.xpath)
+            raise Exception(f"Could not find xpath for {self.xpath}")
 
         tag_help = StringIO()
         tag_help.write("## " + self._pretty_title)
@@ -98,7 +98,7 @@ def _build_tag(tag, hide_attributes):
                     doc = _doc_or_none(element)
                     if doc is None:
                         doc = _doc_or_none(_type_el(element))
-                    assert doc is not None, "Documentation for %s is empty" % element.attrib["name"]
+                    assert doc is not None, f"Documentation for {element.attrib['name']} is empty"
                     doc = doc.strip()
 
                     element_el = _find_tag_el(element)
@@ -110,10 +110,9 @@ def _build_tag(tag, hide_attributes):
     if best_practices := _get_bp_link(annotation_el):
         tag_help.write("\n\n### Best Practices\n")
         tag_help.write(
-            """
-Find the Intergalactic Utilities Commision suggested best practices for this
-element [here](%s)."""
-            % best_practices
+            f"""
+Find the Intergalactic Utilities Commission suggested best practices for this
+element [here]({best_practices})."""
         )
     tag_help.write(_build_attributes_table(tag, attributes, hide_attributes))
 
@@ -140,7 +139,7 @@ def _get_bp_link(annotation_el):
     anchor = annotation_el.attrib.get("{http://galaxyproject.org/xml/1.0}best_practices", None)
     link = None
     if anchor:
-        link = "https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#%s" % anchor
+        link = f"https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#{anchor}"
     return link
 
 
@@ -149,7 +148,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
     attribute_table.write("\n\n")
     if attributes and not hide_attributes:
         header_prefix = "#" * header_level
-        attribute_table.write("\n%s Attributes\n\n" % header_prefix)
+        attribute_table.write(f"\n{header_prefix} Attributes\n\n")
         attribute_table.write("Attribute | Details | Required\n")
         attribute_table.write("--- | --- | ---\n")
         for attribute in attributes:
@@ -159,7 +158,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
             details = _doc_or_none(attribute)
             if details is None:
                 type_el = _type_el(attribute)
-                assert type_el is not None, "No details or type found for %s" % name
+                assert type_el is not None, f"No details or type found for {name}"
                 details = _doc_or_none(type_el)
                 annotation_el = type_el.find("{http://www.w3.org/2001/XMLSchema}annotation")
             else:
@@ -170,10 +169,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
             details = details.replace("|", "\\|").strip()
             best_practices = _get_bp_link(annotation_el)
             if best_practices:
-                details += (
-                    """ Find the Intergalactic Utilities Commision suggested best practices for this element [here](%s)."""
-                    % best_practices
-                )
+                details += f""" Find the Intergalactic Utilities Commission suggested best practices for this element [here]({best_practices})."""
 
             attribute_table.write(f"``{name}`` | {details} | {use}\n")
     return attribute_table.getvalue()
@@ -204,7 +200,7 @@ def _find_attributes(tag):
     for attribute_group in attribute_groups:
         attribute_group_name = attribute_group.get("ref")
         attribute_group_def = xmlschema_doc.find(
-            "//{http://www.w3.org/2001/XMLSchema}attributeGroup/[@name='%s']" % attribute_group_name
+            f"//{{http://www.w3.org/2001/XMLSchema}}attributeGroup/[@name='{attribute_group_name}']"
         )
         attributes.extend(_find_attributes(attribute_group_def))
     return attributes
@@ -219,9 +215,9 @@ def _find_tag_el(tag):
 
 def _type_el(tag):
     element_type = tag.attrib["type"]
-    type_el = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}complexType/[@name='%s']" % element_type)
+    type_el = xmlschema_doc.find(f"//{{http://www.w3.org/2001/XMLSchema}}complexType/[@name='{element_type}']")
     if type_el is None:
-        type_el = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}simpleType/[@name='%s']" % element_type)
+        type_el = xmlschema_doc.find(f"//{{http://www.w3.org/2001/XMLSchema}}simpleType/[@name='{element_type}']")
     return type_el
 
 
diff --git a/lib/galaxy/actions/library.py b/lib/galaxy/actions/library.py
index 5962474bbf20..72b651e1869a 100644
--- a/lib/galaxy/actions/library.py
+++ b/lib/galaxy/actions/library.py
@@ -265,7 +265,7 @@ def _check_path_paste_params(self, params):
             if not os.path.exists(path):
                 bad_paths.append(path)
         if bad_paths:
-            message = 'Invalid paths: "%s".' % '", "'.join(bad_paths)
+            message = 'Invalid paths: "{}".'.format('", "'.join(bad_paths))
             response_code = 400
             return None, response_code, message
         return None
diff --git a/lib/galaxy/auth/providers/ldap_ad.py b/lib/galaxy/auth/providers/ldap_ad.py
index 180f925556c5..5c7e5974100a 100644
--- a/lib/galaxy/auth/providers/ldap_ad.py
+++ b/lib/galaxy/auth/providers/ldap_ad.py
@@ -135,8 +135,8 @@ def check_config(self, username, email, options):
         self.role_search_attribute = options.get(self.role_search_option)
         if self.auto_create_roles_or_groups and self.role_search_attribute is None:
             raise ConfigurationError(
-                "If 'auto-create-roles' or 'auto-create-groups' is True, a '%s' attribute has to"
-                " be provided." % self.role_search_option
+                f"If 'auto-create-roles' or 'auto-create-groups' is True, a '{self.role_search_option}' attribute has to"
+                " be provided."
             )
 
         return ok, failure_mode
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index c69009d47315..e3da3e743e55 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -944,7 +944,8 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
                     log.warning(
                         "The path '%s' for the 'sanitize_allowlist_file' config option is "
                         "deprecated and will be no longer checked in a future release. Please consult "
-                        "the latest version of the sample configuration file." % deprecated
+                        "the latest version of the sample configuration file.",
+                        deprecated,
                     )
                     _sanitize_allowlist_path = deprecated
                     break
@@ -965,7 +966,7 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
         )
         # Searching data libraries
         self.ftp_upload_dir_template = kwargs.get(
-            "ftp_upload_dir_template", "${ftp_upload_dir}%s${ftp_upload_dir_identifier}" % os.path.sep
+            "ftp_upload_dir_template", f"${{ftp_upload_dir}}{os.path.sep}${{ftp_upload_dir_identifier}}"
         )
         # Support older library-specific path paste option but just default to the new
         # allow_path_paste value.
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 679cc6da19db..6e6a5d570177 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -2089,7 +2089,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "HDF5 Model (%s)" % (nice_size(dataset.get_size()))
+            return f"HDF5 Model ({nice_size(dataset.get_size())})"
 
     def display_data(
         self,
@@ -4258,7 +4258,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary pretext file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary pretext file ({nice_size(dataset.get_size())})"
 
 
 class JP2(Binary):
@@ -4302,7 +4302,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary JPEG 2000 file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary JPEG 2000 file ({nice_size(dataset.get_size())})"
 
 
 class Npz(CompressedArchive):
@@ -4356,7 +4356,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary Numpy npz file ({nice_size(dataset.get_size())})"
 
 
 class HexrdImagesNpz(Npz):
@@ -4433,7 +4433,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary Numpy npz file ({nice_size(dataset.get_size())})"
 
 
 class HexrdEtaOmeNpz(Npz):
@@ -4495,7 +4495,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary Numpy npz file ({nice_size(dataset.get_size())})"
 
 
 class FITS(Binary):
@@ -4624,4 +4624,4 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary numpy file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary numpy file ({nice_size(dataset.get_size())})"
diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
index ea2d1b013138..1e343d32ae8b 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
@@ -181,7 +181,7 @@ def __main__():
                     fields = [str(item) for item in (region.chrom, region.start, region.end, name, 0, region.strand)]
                     if force_num_columns is not None and len(fields) != force_num_columns:
                         fields = force_bed_field_count(fields, count, force_num_columns)
-                    out.write("%s\n" % "\t".join(fields))
+                    out.write("{}\n".format("\t".join(fields)))
                 except Exception:
                     skipped_lines += 1
                     if first_skipped_line is None:
diff --git a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
index 0b968f3c7537..aa7252ba1128 100644
--- a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
+++ b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
@@ -24,11 +24,12 @@ def __main__():
                 else:
                     spec_counts[spec] += 1
                 out.write(
-                    "%s\n"
-                    % maf_utilities.get_fasta_header(
-                        c,
-                        {"block_index": count, "species": spec, "sequence_index": spec_counts[spec]},
-                        suffix="%s_%i_%i" % (spec, count, spec_counts[spec]),
+                    "{}\n".format(
+                        maf_utilities.get_fasta_header(
+                            c,
+                            {"block_index": count, "species": spec, "sequence_index": spec_counts[spec]},
+                            suffix="%s_%i_%i" % (spec, count, spec_counts[spec]),
+                        )
                     )
                 )
                 out.write(f"{c.text}\n")
diff --git a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
index 853d57e0172c..66aa9028e58d 100644
--- a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
+++ b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
@@ -20,7 +20,7 @@ def main():
     with open(sys.argv[1]) as in_file, open(sys.argv[2], "w") as out_file:
         try:
             for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)):
-                out_file.write("%s\n" % "\t".join(map(str, fields)))
+                out_file.write("{}\n".format("\t".join(map(str, fields))))
         except UCSCLimitException:
             # Wiggle data was truncated, at the very least need to warn the user.
             sys.stderr.write(
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 2fbac3ff7abe..ee323163c885 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -289,18 +289,18 @@ def as_ucsc_display_file(self, dataset: DatasetProtocol, **kwd) -> Union[FileObj
                     if t < len(elems):
                         strand = cast(str, elems[t])
                     tmp = [elems[c], elems[s], elems[e], name, "0", strand]
-                    fh.write("%s\n" % "\t".join(tmp))
+                    fh.write("{}\n".format("\t".join(tmp)))
             elif n >= 0:  # name column (should) exists
                 for i, elems in enumerate(compression_utils.file_iter(dataset.get_file_name())):
                     name = "region_%i" % i
                     if n >= 0 and n < len(elems):
                         name = cast(str, elems[n])
                     tmp = [elems[c], elems[s], elems[e], name]
-                    fh.write("%s\n" % "\t".join(tmp))
+                    fh.write("{}\n".format("\t".join(tmp)))
             else:
                 for elems in compression_utils.file_iter(dataset.get_file_name()):
                     tmp = [elems[c], elems[s], elems[e]]
-                    fh.write("%s\n" % "\t".join(tmp))
+                    fh.write("{}\n".format("\t".join(tmp)))
             return compression_utils.get_fileobj(fh.name, mode="rb")
 
     def display_peek(self, dataset: DatasetProtocol) -> str:
diff --git a/lib/galaxy/datatypes/neo4j.py b/lib/galaxy/datatypes/neo4j.py
index 608b19c0d9c5..0d6fec174dee 100644
--- a/lib/galaxy/datatypes/neo4j.py
+++ b/lib/galaxy/datatypes/neo4j.py
@@ -30,9 +30,8 @@ def generate_primary_file(self, dataset: HasExtraFilesAndMetadata) -> str:
         """
         # self.regenerate_primary_file(dataset)
         rval = [
-            "<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
+            f"<html><head><title>Files for Composite Dataset ({self.file_ext})</title></head><p/>\
             This composite dataset is composed of the following files:<p/><ul>"
-            % (self.file_ext)
         ]
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             opt_text = ""
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index d691e98f0bfc..f9b30ca3bcfd 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -714,7 +714,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
             if not line.startswith("<?"):
                 break
         # pattern match <root or <ns:root for any ns string
-        pattern = r"<(\w*:)?%s" % self.root
+        pattern = rf"<(\w*:)?{self.root}"
         return re.search(pattern, line) is not None
 
     def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
diff --git a/lib/galaxy/datatypes/qiime2.py b/lib/galaxy/datatypes/qiime2.py
index 0b998bf69c5e..deaaf6a3da47 100644
--- a/lib/galaxy/datatypes/qiime2.py
+++ b/lib/galaxy/datatypes/qiime2.py
@@ -258,10 +258,10 @@ def _get_uuid(path):
     if len(roots) == 0:
         raise ValueError("Archive does not have a visible root directory.")
     if len(roots) > 1:
-        raise ValueError("Archive has multiple root directories: %r" % roots)
+        raise ValueError(f"Archive has multiple root directories: {roots!r}")
     uuid = roots.pop()
     if not _is_uuid4(uuid):
-        raise ValueError("Archive root directory name %r is not a valid version 4 " "UUID." % uuid)
+        raise ValueError(f"Archive root directory name {uuid!r} is not a valid version 4 UUID.")
     return uuid
 
 
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index f91eada60a4b..671f30d82e16 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -971,9 +971,8 @@ def get_extension(self, elem):
         # If extension is not None and is uppercase or mixed case, we need to lowercase it
         if extension is not None and not extension.islower():
             self.log.debug(
-                "%s is not lower case, that could cause troubles in the future. \
-            Please change it to lower case"
-                % extension
+                "%s is not lower case, that could cause troubles in the future. Please change it to lower case",
+                extension,
             )
             extension = extension.lower()
         return extension
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 5865235cfd44..b9b79f046511 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -1075,7 +1075,7 @@ def merge(split_files: List[str], output_file: str) -> None:
     def validate(self, dataset: DatasetProtocol, **kwd) -> DatatypeValidation:
         def validate_row(row):
             if len(row) < 8:
-                raise Exception("Not enough columns in row %s" % row.join("\t"))
+                raise Exception("Not enough columns in row {}".format(row.join("\t")))
 
         validate_tabular(dataset.get_file_name(), sep="\t", validate_row=validate_row, comment_designator="#")
         return DatatypeValidation.validated()
diff --git a/lib/galaxy/datatypes/tracks.py b/lib/galaxy/datatypes/tracks.py
index 0fccbba26d15..e32b035abd4f 100644
--- a/lib/galaxy/datatypes/tracks.py
+++ b/lib/galaxy/datatypes/tracks.py
@@ -36,9 +36,8 @@ def generate_primary_file(self, dataset: HasExtraFilesAndMetadata) -> str:
         cannot rename the datasets here - they come with the default unfortunately
         """
         rval = [
-            "<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
+            f"<html><head><title>Files for Composite Dataset ({self.file_ext})</title></head><p/>\
             This composite dataset is composed of the following files:<p/><ul>"
-            % (self.file_ext)
         ]
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             opt_text = ""
diff --git a/lib/galaxy/datatypes/xml.py b/lib/galaxy/datatypes/xml.py
index a5148336bf80..d3060c93ad9d 100644
--- a/lib/galaxy/datatypes/xml.py
+++ b/lib/galaxy/datatypes/xml.py
@@ -49,7 +49,7 @@ def _has_root_element_in_prefix(self, file_prefix: FilePrefix, root: str) -> boo
             if not line.startswith("<?"):
                 break
         # pattern match <root or <ns:root for any ns string
-        pattern = r"^<(\w*:)?%s" % root
+        pattern = rf"^<(\w*:)?{root}"
         return re.match(pattern, line) is not None
 
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
diff --git a/lib/galaxy/job_execution/actions/post.py b/lib/galaxy/job_execution/actions/post.py
index 75b03cd3e9e6..408ea2accb6c 100644
--- a/lib/galaxy/job_execution/actions/post.py
+++ b/lib/galaxy/job_execution/actions/post.py
@@ -231,11 +231,11 @@ def _gen_new_name(self, action, input_names, replacement_dict):
                     elif operation == "lower":
                         replacement = replacement.lower()
 
-                new_name = new_name.replace("#{%s}" % to_be_replaced, replacement)
+                new_name = new_name.replace(f"#{{{to_be_replaced}}}", replacement)
 
             if replacement_dict:
                 for k, v in replacement_dict.items():
-                    new_name = new_name.replace("${%s}" % k, v)
+                    new_name = new_name.replace(f"${{{k}}}", v)
 
         return new_name
 
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 5ba851359c92..8b0984886312 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -2169,8 +2169,7 @@ def check_limits(self, runtime=None):
                     )
                     return (
                         JobState.runner_states.OUTPUT_SIZE_LIMIT,
-                        "Job output file grew too large (greater than %s), please try different inputs or parameters"
-                        % util.nice_size(self.app.job_config.limits.output_size),
+                        f"Job output file grew too large (greater than {util.nice_size(self.app.job_config.limits.output_size)}), please try different inputs or parameters",
                     )
         if self.app.job_config.limits.walltime_delta is not None and runtime is not None:
             if runtime > self.app.job_config.limits.walltime_delta:
diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
index e87d7c1b0091..54ae6f27f464 100644
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -169,7 +169,7 @@ def run_next(self):
                 try:
                     action_str = f"galaxy.jobs.runners.{self.__class__.__name__.lower()}.{name}"
                     action_timer = self.app.execution_timer_factory.get_timer(
-                        f"internals.{action_str}", "job runner action %s for job ${job_id} executed" % (action_str)
+                        f"internals.{action_str}", f"job runner action {action_str} for job ${{job_id}} executed"
                     )
                     method(arg)
                     log.trace(action_timer.to_str(job_id=job_id))
diff --git a/lib/galaxy/jobs/runners/aws.py b/lib/galaxy/jobs/runners/aws.py
index ee0284fe0f23..57b8dae427fa 100644
--- a/lib/galaxy/jobs/runners/aws.py
+++ b/lib/galaxy/jobs/runners/aws.py
@@ -528,7 +528,7 @@ def parse_destination_params(self, params):
             parsed_params[k] = mapper(value)  # type: ignore[operator]
         if check_required:
             raise AWSBatchRunnerException(
-                "AWSBatchJobRunner requires the following params to be provided: %s." % (", ".join(check_required))
+                "AWSBatchJobRunner requires the following params to be provided: {}.".format(", ".join(check_required))
             )
 
         # parse Platform
diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index a1012d1a3705..4ab56c460ff5 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -13,7 +13,7 @@
     PBS_IMPORT_MESSAGE = (
         "The Python pbs-python package is required to use "
         "this feature, please install it or correct the "
-        "following error:\nImportError %s" % str(exc)
+        f"following error:\nImportError {exc}"
     )
 
 from galaxy import (
@@ -514,7 +514,7 @@ def stop_job(self, job_wrapper):
         try:
             pbs_server_name = self.__get_pbs_server(job.destination_params)
             if pbs_server_name is None:
-                log.debug("(%s) Job queued but no destination stored in job params, cannot delete" % job_tag)
+                log.debug("(%s) Job queued but no destination stored in job params, cannot delete", job_tag)
                 return
             c = pbs.pbs_connect(util.smart_str(pbs_server_name))
             if c <= 0:
diff --git a/lib/galaxy/jobs/runners/state_handlers/resubmit.py b/lib/galaxy/jobs/runners/state_handlers/resubmit.py
index b6bea8e3f467..172237a32f66 100644
--- a/lib/galaxy/jobs/runners/state_handlers/resubmit.py
+++ b/lib/galaxy/jobs/runners/state_handlers/resubmit.py
@@ -62,7 +62,7 @@ def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_stat
         # Is destination needed here, might these be serialized to the database?
         destination = resubmit.get("environment") or resubmit.get("destination")
         log.info(
-            "%s Job will be resubmitted to '%s' because %s at " "the '%s' destination",
+            "%s Job will be resubmitted to '%s' because %s at the '%s' destination",
             job_log_prefix,
             destination,
             MESSAGES[runner_state],
@@ -106,7 +106,7 @@ def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_stat
         if job.params is None:
             job.params = {}
         job_state.runner_state_handled = True
-        info = "This job was resubmitted to the queue because %s on its " "compute resource." % MESSAGES[runner_state]
+        info = f"This job was resubmitted to the queue because {MESSAGES[runner_state]} on its compute resource."
         job_runner.mark_as_resubmitted(job_state, info=info)
         return
 
diff --git a/lib/galaxy/jobs/runners/util/cli/job/lsf.py b/lib/galaxy/jobs/runners/util/cli/job/lsf.py
index 2a5903e4b486..36842bb51bb5 100644
--- a/lib/galaxy/jobs/runners/util/cli/job/lsf.py
+++ b/lib/galaxy/jobs/runners/util/cli/job/lsf.py
@@ -52,7 +52,7 @@ def submit(self, script_file):
         # This should be really handled outside with something like
         # parse_external. Currently CLI runner expect this to just send it in the last position
         # of the string.
-        return "bsub <%s | awk '{ print $2}' | sed 's/[<>]//g'" % script_file
+        return f"bsub <{script_file} | awk '{{ print $2}}' | sed 's/[<>]//g'"
 
     def delete(self, job_id):
         return f"bkill {job_id}"
diff --git a/lib/galaxy/jobs/runners/util/pykube_util.py b/lib/galaxy/jobs/runners/util/pykube_util.py
index 699df65398ac..6fc2c039f741 100644
--- a/lib/galaxy/jobs/runners/util/pykube_util.py
+++ b/lib/galaxy/jobs/runners/util/pykube_util.py
@@ -25,7 +25,7 @@
     K8S_IMPORT_MESSAGE = (
         "The Python pykube package is required to use "
         "this feature, please install it or correct the "
-        "following error:\nImportError %s" % str(exc)
+        f"following error:\nImportError {exc}"
     )
 
 log = logging.getLogger(__name__)
diff --git a/lib/galaxy/managers/interactivetool.py b/lib/galaxy/managers/interactivetool.py
index 4892091eee99..8cec876ba561 100644
--- a/lib/galaxy/managers/interactivetool.py
+++ b/lib/galaxy/managers/interactivetool.py
@@ -69,7 +69,7 @@ def save(self, key, key_type, token, host, port, info=None):
                 try:
                     # Create table
                     c.execute(
-                        """CREATE TABLE %s
+                        f"""CREATE TABLE {DATABASE_TABLE_NAME}
                                  (key text,
                                   key_type text,
                                   token text,
@@ -78,7 +78,6 @@ def save(self, key, key_type, token, host, port, info=None):
                                   info text,
                                   PRIMARY KEY (key, key_type)
                                   )"""
-                        % (DATABASE_TABLE_NAME)
                     )
                 except Exception:
                     pass
@@ -90,11 +89,9 @@ def save(self, key, key_type, token, host, port, info=None):
                         key_type,
                     ),
                 )
-                insert = """INSERT INTO %s
+                insert = f"""INSERT INTO {DATABASE_TABLE_NAME}
                             (key, key_type, token, host, port, info)
-                            VALUES (?, ?, ?, ?, ?, ?)""" % (
-                    DATABASE_TABLE_NAME
-                )
+                            VALUES (?, ?, ?, ?, ?, ?)"""
                 c.execute(
                     insert,
                     (
diff --git a/lib/galaxy/managers/markdown_parse.py b/lib/galaxy/managers/markdown_parse.py
index ab52141fa4e2..7eeef2ba482d 100644
--- a/lib/galaxy/managers/markdown_parse.py
+++ b/lib/galaxy/managers/markdown_parse.py
@@ -71,10 +71,10 @@ class DynamicArguments:
     "invocation_inputs": [],
 }
 GALAXY_FLAVORED_MARKDOWN_CONTAINERS = list(VALID_ARGUMENTS.keys())
-GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r"(?P<container>%s)" % "|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS)
+GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r"(?P<container>{})".format("|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS))
 
 ARG_VAL_REGEX = r"""[\w_\-]+|\"[^\"]+\"|\'[^\']+\'"""
-FUNCTION_ARG = r"\s*[\w\|]+\s*=\s*(?:%s)\s*" % ARG_VAL_REGEX
+FUNCTION_ARG = rf"\s*[\w\|]+\s*=\s*(?:{ARG_VAL_REGEX})\s*"
 # embed commas between arguments
 FUNCTION_MULTIPLE_ARGS = rf"(?P<firstargcall>{FUNCTION_ARG})(?P<restargcalls>(?:,{FUNCTION_ARG})*)"
 FUNCTION_MULTIPLE_ARGS_PATTERN = re.compile(FUNCTION_MULTIPLE_ARGS)
diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py
index af1adc7f6856..009aae3ea762 100644
--- a/lib/galaxy/managers/markdown_util.py
+++ b/lib/galaxy/managers/markdown_util.py
@@ -67,11 +67,11 @@
 log = logging.getLogger(__name__)
 
 ARG_VAL_CAPTURED_REGEX = r"""(?:([\w_\-\|]+)|\"([^\"]+)\"|\'([^\']+)\')"""
-OUTPUT_LABEL_PATTERN = re.compile(r"output=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
-INPUT_LABEL_PATTERN = re.compile(r"input=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
-STEP_LABEL_PATTERN = re.compile(r"step=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
-PATH_LABEL_PATTERN = re.compile(r"path=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
-SIZE_PATTERN = re.compile(r"size=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
+OUTPUT_LABEL_PATTERN = re.compile(rf"output=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+INPUT_LABEL_PATTERN = re.compile(rf"input=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+STEP_LABEL_PATTERN = re.compile(rf"step=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+PATH_LABEL_PATTERN = re.compile(rf"path=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+SIZE_PATTERN = re.compile(rf"size=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
 # STEP_OUTPUT_LABEL_PATTERN = re.compile(r'step_output=([\w_\-]+)/([\w_\-]+)')
 UNENCODED_ID_PATTERN = re.compile(
     r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|implicit_collection_jobs_id|invocation_id)=([\d]+)"
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index eea8ca6d4d0e..1d7ceaeb9bbd 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -195,7 +195,7 @@ def purge(self, user, flush=True):
                 "The configuration of this Galaxy instance does not allow admins to delete or purge users."
             )
         if not user.deleted:
-            raise exceptions.MessageException("User '%s' has not been deleted, so they cannot be purged." % user.email)
+            raise exceptions.MessageException(f"User '{user.email}' has not been deleted, so they cannot be purged.")
         private_role = self.app.security_agent.get_private_user_role(user)
         # Delete History
         for active_history in user.active_histories:
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index d28fcb08353d..4cb9358961c9 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -612,13 +612,10 @@ def calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=F
     if default_usage_dataset_condition.strip():
         default_usage_dataset_condition = f"AND ( {default_usage_dataset_condition} )"
     default_usage = UNIQUE_DATASET_USER_USAGE.format(and_dataset_condition=default_usage_dataset_condition)
-    default_usage = (
-        """
-UPDATE galaxy_user SET disk_usage = (%s)
+    default_usage = f"""
+UPDATE galaxy_user SET disk_usage = ({default_usage})
 WHERE id = :id
 """
-        % default_usage
-    )
     params = {"id": user_id}
     if default_exclude_ids:
         params["exclude_object_store_ids"] = default_exclude_ids
diff --git a/lib/galaxy/model/deferred.py b/lib/galaxy/model/deferred.py
index e7c009ad3645..d73517fb756a 100644
--- a/lib/galaxy/model/deferred.py
+++ b/lib/galaxy/model/deferred.py
@@ -61,9 +61,9 @@ def __init__(self, staging_directory: str):
         self._staging_directory = staging_directory
 
     def transient_paths_for(self, old_dataset: Dataset) -> TransientDatasetPaths:
-        external_filename_basename = "dataset_%s.dat" % str(old_dataset.uuid)
+        external_filename_basename = f"dataset_{old_dataset.uuid}.dat"
         external_filename = os.path.join(self._staging_directory, external_filename_basename)
-        external_extras_basename = "dataset_%s_files" % str(old_dataset.uuid)
+        external_extras_basename = f"dataset_{old_dataset.uuid}_files"
         external_extras = os.path.join(self._staging_directory, external_extras_basename)
         return TransientDatasetPaths(external_filename, external_extras, self._staging_directory)
 
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index dbca1f250f33..e337858493f4 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1621,7 +1621,7 @@ def _read_list_if_exists(self, file_name: str, required: bool = False) -> List[D
             attrs = load(open(file_name))
         else:
             if required:
-                raise Exception("Failed to find file [%s] in model store archive" % file_name)
+                raise Exception(f"Failed to find file [{file_name}] in model store archive")
             attrs = []
         return attrs
 
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index da023ee13bee..62d49420e5e6 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -1513,8 +1513,8 @@ def wraps(self, *args, **kwargs):
                 if c.__name__ == "DiskObjectStore":
                     return getattr(c, func.__name__)(self, *args, **kwargs)
             raise Exception(
-                "Could not call DiskObjectStore's %s method, does your "
-                "Object Store plugin inherit from DiskObjectStore?" % func.__name__
+                f"Could not call DiskObjectStore's {func.__name__} method, does your "
+                "Object Store plugin inherit from DiskObjectStore?"
             )
 
     return wraps
diff --git a/lib/galaxy/objectstore/rucio_extra_clients.py b/lib/galaxy/objectstore/rucio_extra_clients.py
index 36ff04981b3f..500366ee3618 100644
--- a/lib/galaxy/objectstore/rucio_extra_clients.py
+++ b/lib/galaxy/objectstore/rucio_extra_clients.py
@@ -35,7 +35,7 @@ def _delete_item(self, item, forced_schemes, ignore_availability):
             if not self.rses.get(rse):
                 rse_settings = self.rses.setdefault(rse, rsemgr.get_rse_info(rse, vo=self.client.vo))
                 if not ignore_availability and rse_settings["availability_delete"] != 1:
-                    logger(logging.DEBUG, "%s is not available for deletion. No actions have been taken" % rse)
+                    logger(logging.DEBUG, "%s is not available for deletion. No actions have been taken", rse)
                     continue
 
             # protocol handling and deletion
@@ -52,8 +52,8 @@ def _delete_item(self, item, forced_schemes, ignore_availability):
                     success = True
                 except Exception as error:
                     logger(logging.WARNING, "Delete attempt failed")
-                    logger(logging.INFO, "Exception: %s" % str(error), exc_info=True)
-            logger(logging.DEBUG, "Successfully deleted dataset %s" % pfn)
+                    logger(logging.INFO, "Exception: %s", error, exc_info=True)
+            logger(logging.DEBUG, "Successfully deleted dataset %s", pfn)
 
 
 class InPlaceIngestClient(UploadClient):
@@ -107,7 +107,7 @@ def ingest(self, items, summary_file_path=None, traces_copy_out=None, ignore_ava
             if not self.rses.get(rse):
                 rse_settings = self.rses.setdefault(rse, rsemgr.get_rse_info(rse, vo=self.client.vo))
                 if not ignore_availability and rse_settings["availability_write"] != 1:
-                    raise RSEWriteBlocked("%s is not available for writing. No actions have been taken" % rse)
+                    raise RSEWriteBlocked(f"{rse} is not available for writing. No actions have been taken")
 
             dataset_scope = file.get("dataset_scope")
             dataset_name = file.get("dataset_name")
@@ -120,7 +120,7 @@ def ingest(self, items, summary_file_path=None, traces_copy_out=None, ignore_ava
             registered_file_dids.add(f"{file['did_scope']}:{file['did_name']}")
         wrong_dids = registered_file_dids.intersection(registered_dataset_dids)
         if len(wrong_dids):
-            raise InputValidationError("DIDs used to address both files and datasets: %s" % str(wrong_dids))
+            raise InputValidationError(f"DIDs used to address both files and datasets: {wrong_dids}")
         logger(logging.DEBUG, "Input validation done.")
 
         # clear this set again to ensure that we only try to register datasets once
@@ -129,7 +129,7 @@ def ingest(self, items, summary_file_path=None, traces_copy_out=None, ignore_ava
         summary = []
         for file in files:
             basename = file["basename"]
-            logger(logging.INFO, "Preparing upload for file %s" % basename)
+            logger(logging.INFO, "Preparing upload for file %s", basename)
 
             pfn = file.get("pfn")
 
@@ -169,7 +169,7 @@ def ingest(self, items, summary_file_path=None, traces_copy_out=None, ignore_ava
             trace["transferEnd"] = time.time()
             trace["clientState"] = "DONE"
             file["state"] = "A"
-            logger(logging.INFO, "Successfully uploaded file %s" % basename)
+            logger(logging.INFO, "Successfully uploaded file %s", basename)
             self._send_trace(trace)
 
             if summary_file_path:
diff --git a/lib/galaxy/selenium/sizzle.py b/lib/galaxy/selenium/sizzle.py
index 94d9e903b6ae..f3421c697255 100644
--- a/lib/galaxy/selenium/sizzle.py
+++ b/lib/galaxy/selenium/sizzle.py
@@ -87,22 +87,19 @@ def find_elements_by_sizzle(driver, sizzle_selector: str):
 
 
 def _inject_sizzle(driver, sizzle_url, timeout):
-    script = (
-        """
-        if(typeof(window.$) != "undefined") {
+    script = f"""
+        if(typeof(window.$) != "undefined") {{
             // Just reuse jQuery if it is available, avoids potential amd problems
             // that have cropped up with Galaxy for instance.
             window.Sizzle = window.$;
-        } else {
+        }} else {{
             var _s = document.createElement("script");
             _s.type = "text/javascript";
-            _s.src = "%s";
+            _s.src = "{sizzle_url}";
             var _h = document.getElementsByTagName("head")[0];
             _h.appendChild(_s);
-        }
+        }}
     """
-        % sizzle_url
-    )
     driver.execute_script(script)
     wait = WebDriverWait(driver, timeout)
     wait.until(lambda d: _is_sizzle_loaded(d), f"Can't inject Sizzle in {timeout} seconds")
diff --git a/lib/galaxy/tool_shed/tools/tool_validator.py b/lib/galaxy/tool_shed/tools/tool_validator.py
index 1d2780c81d3d..a73af2230c9e 100644
--- a/lib/galaxy/tool_shed/tools/tool_validator.py
+++ b/lib/galaxy/tool_shed/tools/tool_validator.py
@@ -70,10 +70,9 @@ def check_tool_input_params(self, repo_dir, tool_config_name, tool, sample_files
                                 sample_found = True
                                 break
                         if not sample_found:
-                            correction_msg = f"This file refers to a file named <b>{str(index_file_name)}</b>.  "
-                            correction_msg += (
-                                "Upload a file named <b>%s.sample</b> to the repository to correct this error."
-                                % str(index_file_name)
+                            correction_msg = (
+                                f"This file refers to a file named <b>{index_file_name}</b>.  "
+                                f"Upload a file named <b>{index_file_name}.sample</b> to the repository to correct this error."
                             )
                             invalid_files_and_errors_tups.append((tool_config_name, correction_msg))
         return invalid_files_and_errors_tups
diff --git a/lib/galaxy/tool_shed/util/shed_util_common.py b/lib/galaxy/tool_shed/util/shed_util_common.py
index cb16ee71e918..43a1e652b110 100644
--- a/lib/galaxy/tool_shed/util/shed_util_common.py
+++ b/lib/galaxy/tool_shed/util/shed_util_common.py
@@ -163,7 +163,7 @@ def set_image_paths(app, text, encoded_repository_id=None, tool_shed_repository=
         # settings like .. images:: http_files/images/help.png
         for match in re.findall(".. image:: (?!http)/?(.+)", text):
             text = text.replace(match, match.replace("/", "%2F"))
-        text = re.sub(r"\.\. image:: (?!https?://)/?(.+)", r".. image:: %s/\1" % route_to_images, text)
+        text = re.sub(r"\.\. image:: (?!https?://)/?(.+)", rf".. image:: {route_to_images}/\1", text)
     return text
 
 
diff --git a/lib/galaxy/tool_util/deps/brew_exts.py b/lib/galaxy/tool_util/deps/brew_exts.py
index 0f56b279251a..ce2adb760743 100755
--- a/lib/galaxy/tool_util/deps/brew_exts.py
+++ b/lib/galaxy/tool_util/deps/brew_exts.py
@@ -387,9 +387,9 @@ def modify_environ(self, environ):
         if self.action == "set" or not environ.get(self.variable, ""):
             environ[self.variable] = self.__eval("${value}")
         elif self.action == "prepend":
-            environ[self.variable] = self.__eval("${value}:%s" % environ[self.variable])
+            environ[self.variable] = self.__eval(f"${{value}}:{environ[self.variable]}")
         else:
-            environ[self.variable] = self.__eval("%s:${value}" % environ[self.variable])
+            environ[self.variable] = self.__eval(f"{environ[self.variable]}:${{value}}")
 
     def __eval(self, template):
         return string.Template(template).safe_substitute(
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build.py b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
index bcbf1bfdf0bc..be956c84a8b9 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_build.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
@@ -307,7 +307,7 @@ def mull_targets(
         conda_bin = "mamba"
         if mamba_version is None:
             mamba_version = ""
-    involucro_args.extend(["-set", "CONDA_BIN=%s" % conda_bin])
+    involucro_args.extend(["-set", f"CONDA_BIN={conda_bin}"])
     if conda_version is not None or mamba_version is not None:
         mamba_test = "true"
         specs = []
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index ef39fd2ac2d4..57d22e34750e 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -1133,7 +1133,8 @@ def parse_stdio_regexes(self, stdio_elem):
                         log.warning(
                             "Tool id %s: unable to determine if tool "
                             "stream source scanning is output, error, "
-                            "or both. Defaulting to use both." % self.id
+                            "or both. Defaulting to use both.",
+                            self.id,
                         )
                         regex.stdout_match = True
                         regex.stderr_match = True
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 917464e5b45d..6e64d3a11011 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2103,7 +2103,7 @@ def validate_inputs(input, value, error, parent, context, prefixed_name, prefixe
                             )
                         parent[input.name] = value
                     except Exception:
-                        messages[prefixed_name] = "Attempt to replace invalid value for '%s' failed." % (prefixed_label)
+                        messages[prefixed_name] = f"Attempt to replace invalid value for '{prefixed_label}' failed."
                 else:
                     messages[prefixed_name] = error
 
@@ -2315,7 +2315,7 @@ def to_archive(self):
                     if os.path.exists(filesystem_path):
                         tarball_files.append((filesystem_path, tarball_path))
                         image_found = True
-                        tool_xml = tool_xml.replace("${static_path}/%s" % tarball_path, tarball_path)
+                        tool_xml = tool_xml.replace(f"${{static_path}}/{tarball_path}", tarball_path)
         # If one or more tool help images were found, add the modified tool XML to the tarball instead of the original.
         if image_found:
             with tempfile.NamedTemporaryFile(mode="w", suffix=".xml", delete=False) as fh2:
@@ -2684,7 +2684,7 @@ def _compare_tool_version(self, job):
             )
             if tool is None:
                 raise exceptions.MessageException(
-                    "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id
+                    f"This dataset was created by an obsolete tool ({tool_id}). Can't re-run."
                 )
             if (self.id != tool_id and self.old_id != tool_id) or self.version != tool_version:
                 if self.id == tool_id:
diff --git a/lib/galaxy/tools/error_reports/plugins/gitlab.py b/lib/galaxy/tools/error_reports/plugins/gitlab.py
index b8f2d923bade..3540154dfca5 100644
--- a/lib/galaxy/tools/error_reports/plugins/gitlab.py
+++ b/lib/galaxy/tools/error_reports/plugins/gitlab.py
@@ -154,7 +154,7 @@ def submit_report(self, dataset, job, tool, **kwargs):
                         gl_emailquery = self.gitlab.users.list(search=gl_useremail)
                         log.debug(f"GitLab error reporting - User list: {gl_emailquery}")
                         if len(gl_emailquery) > 0:
-                            log.debug("GitLab error reporting - Last Committer user ID: %s" % gl_emailquery[0].get_id())
+                            log.debug("GitLab error reporting - Last Committer user ID: %s", gl_emailquery[0].get_id())
                             self.git_username_id_cache[gl_useremail] = gl_emailquery[0].get_id()
                     gl_userid = self.git_username_id_cache.get(gl_useremail, None)
 
diff --git a/lib/galaxy/util/markdown.py b/lib/galaxy/util/markdown.py
index 3ebaab42202f..fa142df66776 100644
--- a/lib/galaxy/util/markdown.py
+++ b/lib/galaxy/util/markdown.py
@@ -2,7 +2,7 @@
 
 
 def literal_via_fence(content):
-    return "\n%s\n" % "\n".join(f"    {line}" for line in content.splitlines())
+    return "\n{}\n".format("\n".join(f"    {line}" for line in content.splitlines()))
 
 
 def indicate_data_truncated():
diff --git a/lib/galaxy/util/topsort.py b/lib/galaxy/util/topsort.py
index 38bdf40c4bd4..64a1338fa1a4 100644
--- a/lib/galaxy/util/topsort.py
+++ b/lib/galaxy/util/topsort.py
@@ -168,7 +168,7 @@ def topsort(pairlist):
             for y in successors[x]:
                 numpreds[y] = numpreds[y] - 1
                 if numpreds[y] == 0:
-                    answer.append(y)  # noqa: B038
+                    answer.append(y)
             # following "del" isn't needed; just makes
             # CycleError details easier to grasp
             del successors[x]
diff --git a/lib/galaxy/web/framework/middleware/profile.py b/lib/galaxy/web/framework/middleware/profile.py
index da2d4c9f9a8a..649ec2933596 100644
--- a/lib/galaxy/web/framework/middleware/profile.py
+++ b/lib/galaxy/web/framework/middleware/profile.py
@@ -171,7 +171,7 @@ def func_std_string(func_name):
         # special case for built-in functions
         name = func_name[2]
         if name.startswith("<") and name.endswith(">"):
-            return "{%s}" % name[1:-1]
+            return f"{{{name[1:-1]}}}"
         else:
             return name
     else:
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 0029bb70a7e6..0cd502606613 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -144,7 +144,7 @@ def build_apispec(self):
             if rule.routepath.endswith(".:(format)") or not rule.routepath.startswith("api/"):
                 continue
             # Try to replace routes various ways to encode variables with simple swagger {form}
-            swagger_path = "/%s" % RE_URL.sub(r"{\1}", rule.routepath)
+            swagger_path = "/{}".format(RE_URL.sub(r"{\1}", rule.routepath))
             controller = rule.defaults.get("controller", "")
             action = rule.defaults.get("action", "")
             # Get the list of methods for the route
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 0070c9be7c56..7e788bb1cc0f 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -534,7 +534,7 @@ def manage_users_and_groups_for_quota(self, trans, payload=None, **kwd):
                     in_groups.append(trans.security.encode_id(group.id))
                 all_groups.append((group.name, trans.security.encode_id(group.id)))
             return {
-                "title": "Quota '%s'" % quota.name,
+                "title": f"Quota '{quota.name}'",
                 "message": "Quota '%s' is currently associated with %d user(s) and %d group(s)."
                 % (quota.name, len(in_users), len(in_groups)),
                 "status": "info",
@@ -797,7 +797,7 @@ def manage_users_and_groups_for_role(self, trans, payload=None, **kwd):
                     in_groups.append(trans.security.encode_id(group.id))
                 all_groups.append((group.name, trans.security.encode_id(group.id)))
             return {
-                "title": "Role '%s'" % role.name,
+                "title": f"Role '{role.name}'",
                 "message": "Role '%s' is currently associated with %d user(s) and %d group(s)."
                 % (role.name, len(in_users), len(in_groups)),
                 "status": "info",
@@ -902,7 +902,7 @@ def manage_users_and_roles_for_group(self, trans, payload=None, **kwd):
                     in_roles.append(trans.security.encode_id(role.id))
                 all_roles.append((role.name, trans.security.encode_id(role.id)))
             return {
-                "title": "Group '%s'" % group.name,
+                "title": f"Group '{group.name}'",
                 "message": "Group '%s' is currently associated with %d user(s) and %d role(s)."
                 % (group.name, len(in_users), len(in_roles)),
                 "status": "info",
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 69f25c42866a..e1c2f5b79a9a 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -332,7 +332,7 @@ def get_edit(self, trans, dataset_id=None, **kwd):
             }
         else:
             return self.message_exception(
-                trans, "You do not have permission to edit this dataset's ( id: %s ) information." % str(dataset_id)
+                trans, f"You do not have permission to edit this dataset's ( id: {dataset_id} ) information."
             )
 
     @web.expose_api_anonymous
diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index fd3f1a036f20..3db60f29ad2a 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -155,7 +155,7 @@ def permissions(self, trans, payload=None, **kwd):
                         "value": [trans.security.encode_id(role.id) for role in in_roles],
                     }
                 )
-            return {"title": "Change default dataset permissions for history '%s'" % history.name, "inputs": inputs}
+            return {"title": f"Change default dataset permissions for history '{history.name}'", "inputs": inputs}
         else:
             self.history_manager.error_unless_mutable(history)
             permissions = {}
@@ -164,7 +164,7 @@ def permissions(self, trans, payload=None, **kwd):
                 in_roles = [trans.sa_session.get(Role, trans.security.decode_id(x)) for x in in_roles]
                 permissions[trans.app.security_agent.get_action(action.action)] = in_roles
             trans.app.security_agent.history_set_default_permissions(history, permissions)
-            return {"message": "Default history '%s' dataset permissions have been changed." % history.name}
+            return {"message": f"Default history '{history.name}' dataset permissions have been changed."}
 
     @web.legacy_expose_api
     @web.require_login("make datasets private")
@@ -286,10 +286,10 @@ def rename(self, trans, payload=None, **kwd):
                 new_name = payload.get("name_%i" % i)
                 # validate name is empty
                 if not isinstance(new_name, str) or not new_name.strip():
-                    messages.append("You must specify a valid name for History '%s'." % cur_name)
+                    messages.append(f"You must specify a valid name for History '{cur_name}'.")
                 # skip if not the owner
                 elif h.user_id != user.id:
-                    messages.append("History '%s' does not appear to belong to you." % cur_name)
+                    messages.append(f"History '{cur_name}' does not appear to belong to you.")
                 # skip if it wouldn't be a change
                 elif new_name != cur_name:
                     h.name = new_name
diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py
index 0d4d11b993e6..b222c7a6be3e 100644
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -100,7 +100,7 @@ def create(self, trans, payload=None, **kwd):
             }
         else:
             page = self.page_manager.create_page(trans, CreatePagePayload(**payload))
-            return {"message": "Page '%s' successfully created." % page.title, "status": "success"}
+            return {"message": f"Page '{page.title}' successfully created.", "status": "success"}
 
     @web.legacy_expose_api
     @web.require_login("edit pages")
@@ -159,7 +159,7 @@ def edit(self, trans, payload=None, **kwd):
                 trans.sa_session.add(p)
                 with transaction(trans.sa_session):
                     trans.sa_session.commit()
-            return {"message": "Attributes of '%s' successfully saved." % p.title, "status": "success"}
+            return {"message": f"Attributes of '{p.title}' successfully saved.", "status": "success"}
 
     @web.expose
     @web.require_login()
diff --git a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
index f85e9b2d9a30..d3337bb8e602 100644
--- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
@@ -46,9 +46,9 @@ def __get_tool(self, tool_id, tool_version=None, get_loaded_tools_by_lineage=Fal
     def index(self, trans, tool_id=None, from_noframe=None, **kwd):
         def __tool_404__():
             log.debug("index called with tool id '%s' but no such tool exists", tool_id)
-            trans.log_event("Tool id '%s' does not exist" % tool_id)
+            trans.log_event(f"Tool id '{tool_id}' does not exist")
             trans.response.status = 404
-            return trans.show_error_message("Tool '%s' does not exist." % (escape(tool_id)))
+            return trans.show_error_message(f"Tool '{escape(tool_id)}' does not exist.")
 
         # tool id not available, redirect to main page
         if tool_id is None:
diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py
index 157cfde250d2..3928d2e6f02d 100644
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -225,7 +225,7 @@ def edit(self, trans, payload=None, **kwd):
                 trans.sa_session.add(v)
                 with transaction(trans.sa_session):
                     trans.sa_session.commit()
-            return {"message": "Attributes of '%s' successfully saved." % v.title, "status": "success"}
+            return {"message": f"Attributes of '{v.title}' successfully saved.", "status": "success"}
 
     # ------------------------- registry.
     @web.expose
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index e1fcaceeefba..46926aaca35c 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -138,7 +138,7 @@ def to_cwl(value, hda_references, step):
         # I think the following two checks are needed but they may
         # not be needed.
         if not value.dataset.in_ready_state():
-            why = "dataset [%s] is needed for valueFrom expression and is non-ready" % value.id
+            why = f"dataset [{value.id}] is needed for valueFrom expression and is non-ready"
             raise DelayedWorkflowEvaluation(why=why)
         if not value.is_ok:
             raise FailWorkflowEvaluation(
@@ -190,7 +190,7 @@ def from_cwl(value, hda_references, progress: "WorkflowProgress"):
             # This is going to re-file -> HDA this each iteration I think, not a good
             # implementation.
             return progress.raw_to_galaxy(value)
-        assert value["location"].startswith("step_input://"), "Invalid location %s" % value
+        assert value["location"].startswith("step_input://"), f"Invalid location {value}"
         return hda_references[int(value["location"][len("step_input://") :]) - 1]
     elif isinstance(value, dict):
         raise NotImplementedError()
diff --git a/lib/galaxy/workflow/refactor/execute.py b/lib/galaxy/workflow/refactor/execute.py
index d35cbbbc7785..fc38a9351468 100644
--- a/lib/galaxy/workflow/refactor/execute.py
+++ b/lib/galaxy/workflow/refactor/execute.py
@@ -251,7 +251,7 @@ def _apply_extract_input(self, action: ExtractInputAction, execution: RefactorAc
     def _apply_extract_untyped_parameter(self, action: ExtractUntypedParameter, execution: RefactorActionExecution):
         untyped_parameter_name = action.name
         new_label = action.label or untyped_parameter_name
-        target_value = "${%s}" % untyped_parameter_name
+        target_value = f"${{{untyped_parameter_name}}}"
 
         target_tool_inputs = []
         rename_pjas = []
@@ -330,7 +330,7 @@ def callback(input, prefixed_name, context, value=None, **kwargs):
             if untyped_parameter_name != new_label:
                 action_arguments = rename_pja.get("action_arguments")
                 old_newname = action_arguments["newname"]
-                new_newname = old_newname.replace(target_value, "${%s}" % new_label)
+                new_newname = old_newname.replace(target_value, f"${{{new_label}}}")
                 action_arguments["newname"] = new_newname
 
         optional = False
diff --git a/lib/galaxy_test/api/test_libraries.py b/lib/galaxy_test/api/test_libraries.py
index cd1c67926d29..440d004db146 100644
--- a/lib/galaxy_test/api/test_libraries.py
+++ b/lib/galaxy_test/api/test_libraries.py
@@ -194,7 +194,7 @@ def test_create_library_dataset_bootstrap_user(self, library_name="private_datas
         library = self.library_populator.new_private_library(library_name)
         payload, files = self.library_populator.create_dataset_request(library, file_type="txt", contents="create_test")
         create_response = self.galaxy_interactor.post(
-            "libraries/%s/contents" % library["id"], payload, files=files, key=self.master_api_key
+            f"libraries/{library['id']}/contents", payload, files=files, key=self.master_api_key
         )
         self._assert_status_code_is(create_response, 400)
 
diff --git a/lib/tool_shed/dependencies/attribute_handlers.py b/lib/tool_shed/dependencies/attribute_handlers.py
index 87cba9e1a6fd..2d72abd48e17 100644
--- a/lib/tool_shed/dependencies/attribute_handlers.py
+++ b/lib/tool_shed/dependencies/attribute_handlers.py
@@ -137,8 +137,8 @@ def handle_elem(self, elem):
                     elem.attrib["changeset_revision"] = lastest_installable_changeset_revision
                     altered = True
                 else:
-                    error_message = "Invalid latest installable changeset_revision %s " % str(
-                        lastest_installable_changeset_revision
+                    error_message = (
+                        f"Invalid latest installable changeset_revision {lastest_installable_changeset_revision} "
                     )
                     error_message += f"retrieved for repository {name} owned by {owner}.  "
             else:
diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 41fdf8da1821..31a1fc45cac0 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -1036,10 +1036,10 @@ def set_repository_metadata(self, host, content_alert_str="", **kwd):
                         changeset_revisions.append(changeset_revision)
                 self._add_tool_versions(repository_id, repository_metadata, changeset_revisions)
         elif len(repo) == 1 and not self.invalid_file_tups:
-            message = "Revision <b>%s</b> includes no Galaxy utilities for which metadata can " % str(
-                self.repository.tip()
+            message = (
+                f"Revision <b>{self.repository.tip()}</b> includes no Galaxy utilities for which metadata can "
+                "be defined so this revision cannot be automatically installed into a local Galaxy instance."
             )
-            message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."
             status = "error"
         if self.invalid_file_tups:
             message = tool_util.generate_message_for_invalid_tools(
diff --git a/lib/tool_shed/repository_types/util.py b/lib/tool_shed/repository_types/util.py
index dc2751eebc16..fff61e6778f2 100644
--- a/lib/tool_shed/repository_types/util.py
+++ b/lib/tool_shed/repository_types/util.py
@@ -43,26 +43,18 @@ def generate_message_for_repository_type_change(app, repository):
         repository_suite_definition_type_class = app.repository_types_registry.get_class_by_label(
             REPOSITORY_SUITE_DEFINITION
         )
-        message += (
-            "This repository currently contains a single file named <b>%s</b>.  If the intent of this repository is "
-            % REPOSITORY_DEPENDENCY_DEFINITION_FILENAME
-        )
-        message += "to define relationships to a collection of repositories that contain related Galaxy utilities with "
-        message += (
-            "no plans to add additional files, consider setting its type to <b>%s</b>.<br/>"
-            % repository_suite_definition_type_class.label
+        message = (
+            f"This repository currently contains a single file named <b>{REPOSITORY_DEPENDENCY_DEFINITION_FILENAME}</b>.  If the intent of this repository is "
+            "to define relationships to a collection of repositories that contain related Galaxy utilities with "
+            f"no plans to add additional files, consider setting its type to <b>{repository_suite_definition_type_class.label}</b>.<br/>"
         )
     elif repository.can_change_type_to(app, TOOL_DEPENDENCY_DEFINITION):
         tool_dependency_definition_type_class = app.repository_types_registry.get_class_by_label(
             TOOL_DEPENDENCY_DEFINITION
         )
-        message += (
-            "This repository currently contains a single file named <b>%s</b>.  If additional files will "
-            % TOOL_DEPENDENCY_DEFINITION_FILENAME
-        )
-        message += (
-            "not be added to this repository, consider setting its type to <b>%s</b>.<br/>"
-            % tool_dependency_definition_type_class.label
+        message = (
+            f"This repository currently contains a single file named <b>{TOOL_DEPENDENCY_DEFINITION_FILENAME}</b>.  If additional files will "
+            f"not be added to this repository, consider setting its type to <b>{tool_dependency_definition_type_class.label}</b>.<br/>"
         )
     return message
 
diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 30d6525ec192..87eaf2c3ab8d 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -2048,9 +2048,7 @@ def assert_has():
     def _assert_repo_has_tool_with_id(
         self, installed_repository: galaxy_model.ToolShedRepository, tool_id: str
     ) -> None:
-        assert "tools" in installed_repository.metadata_, (
-            "No valid tools were defined in %s." % installed_repository.name
-        )
+        assert "tools" in installed_repository.metadata_, f"No valid tools were defined in {installed_repository.name}."
         tools = installed_repository.metadata_["tools"]
         found_it = False
         for tool in tools:  # type:ignore[attr-defined]
@@ -2064,9 +2062,9 @@ def _assert_repo_has_tool_with_id(
     def _assert_repo_has_invalid_tool_in_file(
         self, installed_repository: galaxy_model.ToolShedRepository, name: str
     ) -> None:
-        assert "invalid_tools" in installed_repository.metadata_, (
-            "No invalid tools were defined in %s." % installed_repository.name
-        )
+        assert (
+            "invalid_tools" in installed_repository.metadata_
+        ), f"No invalid tools were defined in {installed_repository.name}."
         invalid_tools = installed_repository.metadata_["invalid_tools"]
         found_it = name in invalid_tools
         assert found_it, f"Did not find invalid tool file {name} in {invalid_tools}"
diff --git a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
index 9eb9d9b7aa94..4b540f71584e 100644
--- a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
+++ b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
@@ -165,15 +165,14 @@ def test_0025_delete_repository_dependency(self):
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that contains repository_dependencies.xml is no longer downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that contains repository_dependencies.xml is no longer downloadable."
         # Check that the new tip is also downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that does not contain repository_dependencies.xml is not downloadable."
-            % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that does not contain repository_dependencies.xml is not downloadable."
         # Verify that there are only two downloadable revisions.
         assert (
             len(self._db_repository(repository).downloadable_revisions) == 2
@@ -279,14 +278,14 @@ def test_0050_delete_complex_repository_dependency(self):
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that contains tool_dependencies.xml is no longer downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that contains tool_dependencies.xml is no longer downloadable."
         # Check that the new tip is also downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that does not contain tool_dependencies.xml is not downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that does not contain tool_dependencies.xml is not downloadable."
         # Verify that there are only two downloadable revisions.
         assert (
             len(self._db_repository(repository).downloadable_revisions) == 2
@@ -331,9 +330,9 @@ def test_0060_delete_bwa_tool_dependency_definition(self):
         assert old_changeset_revision != new_changeset_revision
         # Check that the old changeset revision is still downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that contains tool_dependencies.xml is no longer downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that contains tool_dependencies.xml is no longer downloadable."
         # Check that the new tip does not have a metadata revision.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
         # If a changeset revision does not have metadata, the above method will return None.
@@ -364,15 +363,14 @@ def test_0065_reupload_bwa_tool_dependency_definition(self):
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record is None, (
-            "The revision of %s that does not contain tool_dependencies.xml should not be downloadable, but is."
-            % repository.name
-        )
+        assert (
+            metadata_record is None
+        ), f"The revision of {repository.name} that does not contain tool_dependencies.xml should not be downloadable, but is."
         # Check that the new tip is also downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that contains tool_dependencies.xml is not downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that contains tool_dependencies.xml is not downloadable."
         # Verify that there are only two downloadable revisions.
         assert (
             len(self._db_repository(repository).downloadable_revisions) == 1
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index a6cab6cc954d..b3fbbb477532 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -136,20 +136,14 @@ def get_repository_file_contents(app: "ToolShedApp", file_path: str, repository_
                 safe_str = f"{safe_str}{basic_util.to_html_string(line)}"
                 # Stop reading after string is larger than MAX_CONTENT_SIZE.
                 if len(safe_str) > MAX_CONTENT_SIZE:
-                    large_str = (
-                        "<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>"
-                        % util.nice_size(MAX_CONTENT_SIZE)
-                    )
+                    large_str = f"<br/>File contents truncated because file size is larger than maximum viewing size of {util.nice_size(MAX_CONTENT_SIZE)}<br/>"
                     safe_str = f"{safe_str}{large_str}"
                     break
 
         if len(safe_str) > basic_util.MAX_DISPLAY_SIZE:
             # Eliminate the middle of the file to display a file no larger than basic_util.MAX_DISPLAY_SIZE.
             # This may not be ideal if the file is larger than MAX_CONTENT_SIZE.
-            join_by_str = (
-                "<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of %s...<br/><br/>"
-                % util.nice_size(basic_util.MAX_DISPLAY_SIZE)
-            )
+            join_by_str = f"<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of {util.nice_size(basic_util.MAX_DISPLAY_SIZE)}...<br/><br/>"
             safe_str = util.shrink_string_by_size(
                 safe_str,
                 basic_util.MAX_DISPLAY_SIZE,
diff --git a/lib/tool_shed/webapp/controllers/user.py b/lib/tool_shed/webapp/controllers/user.py
index 2740ee9f6c7d..eb9a11878eba 100644
--- a/lib/tool_shed/webapp/controllers/user.py
+++ b/lib/tool_shed/webapp/controllers/user.py
@@ -85,8 +85,9 @@ def login(self, trans, refresh_frames=None, **kwd):
         if not success and not user and trans.app.config.require_login:
             if trans.app.config.allow_user_creation:
                 create_account_str = (
-                    "  If you don't already have an account, <a href='%s'>you may create one</a>."
-                    % web.url_for(controller="user", action="create", cntrller="user")
+                    "  If you don't already have an account, <a href='{}'>you may create one</a>.".format(
+                        web.url_for(controller="user", action="create", cntrller="user")
+                    )
                 )
                 header = REQUIRE_LOGIN_TEMPLATE % ("Galaxy tool shed", create_account_str)
             else:
@@ -243,9 +244,9 @@ def reset_password(self, trans, email=None, **kwd):
             if not message:
                 # Default to a non-userinfo-leaking response message
                 message = (
-                    "Your reset request for %s has been received.  "
+                    f"Your reset request for {escape(email)} has been received.  "
                     "Please check your email account for more instructions.  "
-                    "If you do not receive an email shortly, please contact an administrator." % (escape(email))
+                    "If you do not receive an email shortly, please contact an administrator."
                 )
                 reset_user = get_user_by_email(trans.sa_session, email, trans.app.model.User)
                 if not reset_user:
@@ -476,9 +477,7 @@ def change_password(self, trans, token=None, id=None, **kwd):
     @web.expose
     def logout(self, trans, logout_all=False, **kwd):
         trans.handle_user_logout(logout_all=logout_all)
-        message = 'You have been logged out.<br>To log in again <a target="_top" href="%s">go to the home page</a>.' % (
-            url_for("/")
-        )
+        message = f'You have been logged out.<br>To log in again <a target="_top" href="{url_for("/")}">go to the home page</a>.'
         if trans.app.config.use_remote_user and trans.app.config.remote_user_logout_href:
             trans.response.send_redirect(trans.app.config.remote_user_logout_href)
         else:
diff --git a/scripts/api/common.py b/scripts/api/common.py
index 9dca44f367fb..7a9cc62b6ec9 100644
--- a/scripts/api/common.py
+++ b/scripts/api/common.py
@@ -36,7 +36,7 @@ def get(api_key, url):
     try:
         return json.loads(urlopen(url).read())
     except ValueError as e:
-        print("URL did not return JSON data: %s" % e)
+        print(f"URL did not return JSON data: {e}")
         sys.exit(1)
 
 
@@ -87,14 +87,14 @@ def display(api_key, url, return_formatted=True):
         print("------------------")
         for n, i in enumerate(r):
             if isinstance(i, str):
-                print("  %s" % i)
+                print(f"  {i}")
             else:
                 # All collection members should have a name in the response.
                 # url is optional
                 if "url" in i:
                     print("#%d: %s" % (n + 1, i.pop("url")))
                 if "name" in i:
-                    print("  name: %s" % i.pop("name"))
+                    print(f"  name: {i.pop('name')}")
                 try:
                     for k, v in i.items():
                         print(f"  {k}: {v}")
@@ -112,7 +112,7 @@ def display(api_key, url, return_formatted=True):
     elif isinstance(r, str):
         print(r)
     else:
-        print("response is unknown type: %s" % type(r))
+        print(f"response is unknown type: {type(r)}")
 
 
 def submit(api_key, url, data, return_formatted=True):
@@ -143,7 +143,7 @@ def submit(api_key, url, data, return_formatted=True):
                 else:
                     print("----")
                 if "name" in i:
-                    print("  name: %s" % i.pop("name"))
+                    print(f"  name: {i.pop('name')}")
                 for k, v in i.items():
                     print(f"  {k}: {v}")
             else:
diff --git a/scripts/api/data_manager_example_execute.py b/scripts/api/data_manager_example_execute.py
index 5e7e7dc28843..9ece98404625 100644
--- a/scripts/api/data_manager_example_execute.py
+++ b/scripts/api/data_manager_example_execute.py
@@ -47,7 +47,7 @@ def run_tool(tool_id, history_id, params, api_key, galaxy_url, wait=True, sleep_
 
 
 def get_dataset_state(hda_id, api_key, galaxy_url):
-    datasets_url = urljoin(galaxy_url, "api/datasets/%s" % hda_id)
+    datasets_url = urljoin(galaxy_url, f"api/datasets/{hda_id}")
     dataset_info = get(api_key, datasets_url)
     return dataset_info["state"]
 
@@ -117,7 +117,7 @@ def dataset_is_terminal(hda_id, api_key, galaxy_url):
                 wait=False,
             )
         else:
-            "dbkey (%s) was specified more than once, skipping additional specification." % (dbkey)
+            f"dbkey ({dbkey}) was specified more than once, skipping additional specification."
 
     print("Genomes Queued for downloading.")
 
diff --git a/scripts/api/display.py b/scripts/api/display.py
index d46266c2a9ce..6e3513e9d284 100755
--- a/scripts/api/display.py
+++ b/scripts/api/display.py
@@ -9,7 +9,7 @@
 try:
     display(*sys.argv[1:3])
 except TypeError as e:
-    print("usage: %s key url" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url")
     print(e)
     sys.exit(1)
 except URLError as e:
diff --git a/scripts/api/example_watch_folder.py b/scripts/api/example_watch_folder.py
index dd11c594022f..5e12bfd530d6 100755
--- a/scripts/api/example_watch_folder.py
+++ b/scripts/api/example_watch_folder.py
@@ -33,11 +33,11 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
         lib_create_data = {"name": data_library}
         library = submit(api_key, api_url + "libraries", lib_create_data, return_formatted=False)
         library_id = library[0]["id"]
-    folders = display(api_key, api_url + "libraries/%s/contents" % library_id, return_formatted=False)
+    folders = display(api_key, api_url + f"libraries/{library_id}/contents", return_formatted=False)
     for f in folders:
         if f["name"] == "/":
             library_folder_id = f["id"]
-    workflow = display(api_key, api_url + "workflows/%s" % workflow, return_formatted=False)
+    workflow = display(api_key, api_url + f"workflows/{workflow}", return_formatted=False)
     if not workflow:
         print("Workflow %s not found, terminating.")
         sys.exit(1)
@@ -57,7 +57,7 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
                 data["upload_option"] = "upload_paths"
                 data["filesystem_paths"] = fullpath
                 data["create_type"] = "file"
-                libset = submit(api_key, api_url + "libraries/%s/contents" % library_id, data, return_formatted=False)
+                libset = submit(api_key, api_url + f"libraries/{library_id}/contents", data, return_formatted=False)
                 # TODO Handle this better, but the datatype isn't always
                 # set for the followup workflow execution without this
                 # pause.
@@ -88,6 +88,6 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
         data_library = sys.argv[5]
         workflow = sys.argv[6]
     except IndexError:
-        print("usage: %s key url in_folder out_folder data_library workflow" % os.path.basename(sys.argv[0]))
+        print(f"usage: {os.path.basename(sys.argv[0])} key url in_folder out_folder data_library workflow")
         sys.exit(1)
     main(api_key, api_url, in_folder, out_folder, data_library, workflow)
diff --git a/scripts/api/filter_failed_datasets_from_collection.py b/scripts/api/filter_failed_datasets_from_collection.py
index 87fc85f30578..1e66a8b7648d 100644
--- a/scripts/api/filter_failed_datasets_from_collection.py
+++ b/scripts/api/filter_failed_datasets_from_collection.py
@@ -16,8 +16,7 @@
 
 if len(sys.argv) < 5:
     print(
-        "Usage: %s <GalaxyUrl> <ApiKey> <HistoryName (must be unique)> <CollectionHistoryId (i.e. the simple integer id)>"
-        % sys.argv[0]
+        f"Usage: {sys.argv[0]} <GalaxyUrl> <ApiKey> <HistoryName (must be unique)> <CollectionHistoryId (i.e. the simple integer id)>"
     )
     exit(0)
 
diff --git a/scripts/api/history_create_history.py b/scripts/api/history_create_history.py
index 210311324e60..df576a9cd9ba 100644
--- a/scripts/api/history_create_history.py
+++ b/scripts/api/history_create_history.py
@@ -8,7 +8,7 @@
 try:
     assert sys.argv[2]
 except IndexError:
-    print("usage: %s key url [name] " % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url [name] ")
     sys.exit(1)
 try:
     data = {}
diff --git a/scripts/api/history_delete_history.py b/scripts/api/history_delete_history.py
index 2c48d5a45331..6b11b2bbffff 100644
--- a/scripts/api/history_delete_history.py
+++ b/scripts/api/history_delete_history.py
@@ -8,7 +8,7 @@
 try:
     assert sys.argv[2]
 except IndexError:
-    print("usage: %s key url [purge (true/false)] " % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url [purge (true/false)] ")
     sys.exit(1)
 try:
     data = {}
diff --git a/scripts/api/import_library_dataset_to_history.py b/scripts/api/import_library_dataset_to_history.py
index 75d0e8a9095e..c3440c5de51b 100644
--- a/scripts/api/import_library_dataset_to_history.py
+++ b/scripts/api/import_library_dataset_to_history.py
@@ -10,7 +10,7 @@
     data = {}
     data["from_ld_id"] = sys.argv[3]
 except IndexError:
-    print("usage: %s key url library_file_id" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url library_file_id")
     print("    library_file_id is from /api/libraries/<library_id>/contents/<library_file_id>")
     sys.exit(1)
 
diff --git a/scripts/api/library_create_folder.py b/scripts/api/library_create_folder.py
index 8df85a5f46d9..e77bc27511d3 100755
--- a/scripts/api/library_create_folder.py
+++ b/scripts/api/library_create_folder.py
@@ -11,7 +11,7 @@
     data["name"] = sys.argv[4]
     data["create_type"] = "folder"
 except IndexError:
-    print("usage: %s key url folder_id name [description]" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url folder_id name [description]")
     sys.exit(1)
 try:
     data["description"] = sys.argv[5]
diff --git a/scripts/api/library_create_library.py b/scripts/api/library_create_library.py
index b9485c2b1554..514a7129cded 100755
--- a/scripts/api/library_create_library.py
+++ b/scripts/api/library_create_library.py
@@ -9,7 +9,7 @@
     data = {}
     data["name"] = sys.argv[3]
 except IndexError:
-    print("usage: %s key url name [description] [synopsys]" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url name [description] [synopsys]")
     sys.exit(1)
 try:
     data["description"] = sys.argv[4]
diff --git a/scripts/api/library_upload_from_import_dir.py b/scripts/api/library_upload_from_import_dir.py
index 09a42a91d127..a9678eb5937e 100755
--- a/scripts/api/library_upload_from_import_dir.py
+++ b/scripts/api/library_upload_from_import_dir.py
@@ -18,7 +18,7 @@
     data["upload_option"] = "upload_directory"
     data["create_type"] = "file"
 except IndexError:
-    print("usage: %s key url folder_id file_type server_dir dbkey" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url folder_id file_type server_dir dbkey")
     sys.exit(1)
 
 submit(sys.argv[1], sys.argv[2], data)
diff --git a/scripts/api/load_data_with_metadata.py b/scripts/api/load_data_with_metadata.py
index 47e6a7080f12..ee24fbc0f2f5 100755
--- a/scripts/api/load_data_with_metadata.py
+++ b/scripts/api/load_data_with_metadata.py
@@ -39,7 +39,7 @@ def load_file(fullpath, api_key, api_url, library_id, library_folder_id, uuid_fi
     if uuid_field is not None and uuid_field in ext_meta:
         data["uuid"] = ext_meta[uuid_field]
 
-    libset = submit(api_key, api_url + "libraries/%s/contents" % library_id, data, return_formatted=True)
+    libset = submit(api_key, api_url + f"libraries/{library_id}/contents", data, return_formatted=True)
     print(libset)
 
 
@@ -54,7 +54,7 @@ def main(api_key, api_url, in_folder, data_library, uuid_field=None):
         lib_create_data = {"name": data_library}
         library = submit(api_key, api_url + "libraries", lib_create_data, return_formatted=False)
         library_id = library["id"]
-    folders = display(api_key, api_url + "libraries/%s/contents" % library_id, return_formatted=False)
+    folders = display(api_key, api_url + f"libraries/{library_id}/contents", return_formatted=False)
     for f in folders:
         if f["name"] == "/":
             library_folder_id = f["id"]
diff --git a/scripts/api/reset_metadata_on_installed_repositories.py b/scripts/api/reset_metadata_on_installed_repositories.py
index 150f809c0a44..69cdd09d8cb7 100644
--- a/scripts/api/reset_metadata_on_installed_repositories.py
+++ b/scripts/api/reset_metadata_on_installed_repositories.py
@@ -15,7 +15,7 @@
 
 def main(options):
     base_galaxy_url = options.galaxy_url.rstrip("/")
-    url = "%s/api/tool_shed_repositories/reset_metadata_on_installed_repositories" % base_galaxy_url
+    url = f"{base_galaxy_url}/api/tool_shed_repositories/reset_metadata_on_installed_repositories"
     submit(options.api, url, {})
 
 
diff --git a/scripts/api/workflow_delete.py b/scripts/api/workflow_delete.py
index 9972a9b1359c..3ccea68a017d 100644
--- a/scripts/api/workflow_delete.py
+++ b/scripts/api/workflow_delete.py
@@ -17,7 +17,7 @@
 try:
     assert sys.argv[2]
 except IndexError:
-    print("usage: %s key url [purge (true/false)] " % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url [purge (true/false)] ")
     sys.exit(1)
 try:
     data = {}
diff --git a/scripts/api/workflow_execute.py b/scripts/api/workflow_execute.py
index 18824704d92e..a8def8bf8867 100755
--- a/scripts/api/workflow_execute.py
+++ b/scripts/api/workflow_execute.py
@@ -24,7 +24,7 @@ def main():
             step, src, ds_id = v.split("=")
             data["ds_map"][step] = {"src": src, "id": ds_id}
     except IndexError:
-        print("usage: %s key url workflow_id history step=src=dataset_id" % os.path.basename(sys.argv[0]))
+        print(f"usage: {os.path.basename(sys.argv[0])} key url workflow_id history step=src=dataset_id")
         sys.exit(1)
     submit(sys.argv[1], sys.argv[2], data)
 
diff --git a/scripts/api/workflow_execute_parameters.py b/scripts/api/workflow_execute_parameters.py
index 280976f8d3f5..a9693869ee21 100644
--- a/scripts/api/workflow_execute_parameters.py
+++ b/scripts/api/workflow_execute_parameters.py
@@ -46,7 +46,7 @@ def main():
                     print("TOOL ID ERROR:")
 
     except IndexError:
-        print("usage: %s key url workflow_id history step=src=dataset_id" % os.path.basename(sys.argv[0]))
+        print(f"usage: {os.path.basename(sys.argv[0])} key url workflow_id history step=src=dataset_id")
         sys.exit(1)
     submit(sys.argv[1], sys.argv[2], data)
 
diff --git a/scripts/api/workflow_import.py b/scripts/api/workflow_import.py
index 1f78d9567518..98d1a68e6b69 100755
--- a/scripts/api/workflow_import.py
+++ b/scripts/api/workflow_import.py
@@ -14,14 +14,14 @@
 def main():
     api_key = sys.argv[1]
     api_base_url = sys.argv[2]
-    api_url = "%s/api/workflows" % api_base_url
+    api_url = f"{api_base_url}/api/workflows"
     try:
         data = {}
         data["installed_repository_file"] = sys.argv[3]
         if len(sys.argv) > 4 and sys.argv[4] == "--add_to_menu":
             data["add_to_menu"] = True
     except IndexError:
-        print("usage: %s key galaxy_url workflow_file" % os.path.basename(sys.argv[0]))
+        print(f"usage: {os.path.basename(sys.argv[0])} key galaxy_url workflow_file")
         sys.exit(1)
     submit(api_key, api_url, data, return_formatted=False)
 
diff --git a/scripts/api/workflow_import_from_file_rpark.py b/scripts/api/workflow_import_from_file_rpark.py
index 31242d8b25db..47508311c765 100644
--- a/scripts/api/workflow_import_from_file_rpark.py
+++ b/scripts/api/workflow_import_from_file_rpark.py
@@ -20,7 +20,7 @@ def openWorkflow(in_file):
 try:
     assert sys.argv[2]
 except IndexError:
-    print("usage: %s key url [name] " % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url [name] ")
     sys.exit(1)
 try:
     data = {}
diff --git a/scripts/apply_tags.py b/scripts/apply_tags.py
index fa4ebb258bb3..bec742db8ab9 100644
--- a/scripts/apply_tags.py
+++ b/scripts/apply_tags.py
@@ -29,12 +29,12 @@ def read_galaxy_history(self):
             try:
                 update_history = history.show_history(self.history_id)
             except Exception as exception:
-                print("Some problem occurred with history: %s" % self.history_id)
+                print(f"Some problem occurred with history: {self.history_id}")
                 print(exception)
                 return
         update_history_id = update_history["id"]
-        print("History name: %s" % update_history["name"])
-        print("History id: %s" % update_history_id)
+        print(f"History name: {update_history['name']}")
+        print(f"History id: {update_history_id}")
         self.find_dataset_parents_update_tags(history, job, update_history_id)
 
     def find_dataset_parents_update_tags(self, history, job, history_id):
diff --git a/scripts/build_toolbox.py b/scripts/build_toolbox.py
index d471bc9b8d77..f26e571dcb9e 100644
--- a/scripts/build_toolbox.py
+++ b/scripts/build_toolbox.py
@@ -141,7 +141,7 @@ def scanfiles(filenamelist):
             newtoolelement = ET.Element("tool", attrib)
             toolboxpositionelements = toolelement.findall("toolboxposition")
             if not toolboxpositionelements:
-                print("DBG> %s has no toolboxposition" % fn)
+                print(f"DBG> {fn} has no toolboxposition")
             else:
                 for toolboxpositionelement in toolboxpositionelements:
                     toolbox.add(newtoolelement, toolboxpositionelement)
diff --git a/scripts/check_python.py b/scripts/check_python.py
index 62a8cfbfa59e..766d67904fe2 100644
--- a/scripts/check_python.py
+++ b/scripts/check_python.py
@@ -3,6 +3,8 @@
 message to stderr and returns 1
 """
 
+from __future__ import print_function  # noqa: UP010
+
 import sys
 
 
@@ -13,13 +15,12 @@ def check_python():
     else:
         version_string = ".".join(str(_) for _ in sys.version_info[:3])
         msg = (
-            """\
-ERROR: Your Python version is: %s
+            """ERROR: Your Python version is: %s
 Galaxy is currently supported on Python >=3.8 .
 To run Galaxy, please install a supported Python version.
 If a supported version is already installed but is not your default,
 https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
-on how to force Galaxy to use a different version."""
+on how to force Galaxy to use a different version."""  # noqa: UP031
             % version_string
         )
         print(msg, file=sys.stderr)
diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index f9050c58e87e..5c78ff0382b3 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -151,7 +151,7 @@ def main():
     template_file = args.template
     if template_file is None:
         default_template = os.path.join(scriptdir, "admin_cleanup_deletion_template.txt")
-        sample_template_file = "%s.sample" % default_template
+        sample_template_file = f"{default_template}.sample"
         if os.path.exists(default_template):
             template_file = default_template
         elif os.path.exists(sample_template_file):
@@ -164,7 +164,7 @@ def main():
                 "found, please specify template as an option (--template)."
             )
     elif not os.path.exists(template_file):
-        parser.error("Specified template file (%s) not found." % template_file)
+        parser.error(f"Specified template file ({template_file}) not found.")
 
     config = galaxy.config.Configuration(**app_properties)
 
@@ -273,9 +273,9 @@ def administrative_delete_datasets(
         subject = "Galaxy Server Cleanup " "- %d datasets DELETED" % len(dataset_list)
         fromaddr = config.email_from
         print()
-        print("From: %s" % fromaddr)
-        print("To: %s" % email)
-        print("Subject: %s" % subject)
+        print(f"From: {fromaddr}")
+        print(f"To: {email}")
+        print(f"Subject: {subject}")
         print("----------")
         print(msgtext)
         if not info_only:
diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py
index 7ff09d7c4a5a..325cd6b24b08 100755
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -143,22 +143,22 @@ def __open_log(self):
         else:
             logf = os.path.join(self._log_dir, self.name + ".log")
         if self._dry_run:
-            log.info("--dry-run specified, logging changes to stderr instead of log file: %s" % logf)
+            log.info("--dry-run specified, logging changes to stderr instead of log file: %s", logf)
             h = set_log_handler()
         else:
-            log.info("Opening log file: %s" % logf)
+            log.info("Opening log file: %s", logf)
             h = set_log_handler(filename=logf)
         h.setLevel(logging.DEBUG if self._debug else logging.INFO)
         h.setFormatter(LevelFormatter())
         self.__log = logging.getLogger(self.name)
         self.__log.addHandler(h)
         self.__log.propagate = False
-        m = ("==== Log opened: %s " % datetime.datetime.now().isoformat()).ljust(72, "=")
+        m = (f"==== Log opened: {datetime.datetime.now().isoformat()} ").ljust(72, "=")
         self.__log.info(m)
-        self.__log.info(f"Epoch time for this action: {self._epoch_time}")
+        self.__log.info("Epoch time for this action: %s", self._epoch_time)
 
     def __close_log(self):
-        m = ("==== Log closed: %s " % datetime.datetime.now().isoformat()).ljust(72, "=")
+        m = (f"==== Log closed: {datetime.datetime.now().isoformat()} ").ljust(72, "=")
         self.log.info(m)
         self.__log = None
 
@@ -1221,7 +1221,7 @@ def conn(self):
             self.__conn = psycopg2.connect(cursor_factory=NamedTupleCursor, **args)
             # TODO: is this per session or cursor?
             if self.args.work_mem is not None:
-                log.info("Setting work_mem to %s" % self.args.work_mem)
+                log.info("Setting work_mem to %s", self.args.work_mem)
                 self.__conn.cursor().execute("SET work_mem TO %s", (self.args.work_mem,))
         return self.__conn
 
@@ -1271,7 +1271,7 @@ def __parse_args(self):
             nargs="*",
             metavar="ACTION",
             default=[],
-            help="Action(s) to perform, chosen from: %s" % ", ".join(sorted(self.actions.keys())),
+            help="Action(s) to perform, chosen from: {}".format(", ".join(sorted(self.actions.keys()))),
         )
         self.args = parser.parse_args()
 
@@ -1292,7 +1292,7 @@ def __validate_actions(self):
         ok = True
         for name in self.args.actions:
             if name not in self.actions.keys():
-                log.error("Unknown action in sequence: %s" % name)
+                log.error("Unknown action in sequence: %s", name)
                 ok = False
         if not ok:
             log.critical("Exiting due to previous error(s)")
@@ -1381,7 +1381,7 @@ def run(self):
             self.__current_action = name
             with cls(self) as action:
                 self._run_action(action)
-            log.info("Finished %s" % name)
+            log.info("Finished %s", name)
 
 
 if __name__ == "__main__":
diff --git a/scripts/config_sample_to_kwalify.py b/scripts/config_sample_to_kwalify.py
index 5ced81c081fa..6d7357751c06 100644
--- a/scripts/config_sample_to_kwalify.py
+++ b/scripts/config_sample_to_kwalify.py
@@ -55,14 +55,14 @@ def print_line(line):
             type = "str"
     if default == "None":
         default = None
-    print_line("%s:" % key)
-    print_line("  type: %s" % type)
+    print_line(f"{key}:")
+    print_line(f"  type: {type}")
     if default is not None:
-        print_line("  default: %s" % default)
+        print_line(f"  default: {default}")
     # print_line("  required: false")
     print_line("  desc: |")
     for line in current_section_desc:
-        print_line("    %s" % line)
+        print_line(f"    {line}")
     print_line("")
 
 
diff --git a/scripts/db_shell.py b/scripts/db_shell.py
index e1a1da3455bc..44e8803f58de 100644
--- a/scripts/db_shell.py
+++ b/scripts/db_shell.py
@@ -85,7 +85,7 @@ def render_literal_value(self, value, type_):
             """
             if isinstance(value, str):
                 value = value.replace("'", "''")
-                return "'%s'" % value
+                return f"'{value}'"
             elif value is None:
                 return "NULL"
             elif isinstance(value, (float, int)):
@@ -93,10 +93,10 @@ def render_literal_value(self, value, type_):
             elif isinstance(value, decimal.Decimal):
                 return str(value)
             elif isinstance(value, datetime.datetime):
-                return "TO_DATE('%s','YYYY-MM-DD HH24:MI:SS')" % value.strftime("%Y-%m-%d %H:%M:%S")
+                return f"TO_DATE('{value.strftime('%Y-%m-%d %H:%M:%S')}','YYYY-MM-DD HH24:MI:SS')"
 
             else:
-                raise NotImplementedError("Don't know how to literal-quote value %r" % value)
+                raise NotImplementedError(f"Don't know how to literal-quote value {value!r}")
 
     compiler = LiteralCompiler(dialect, statement)
     print(compiler.process(statement))
diff --git a/scripts/drmaa_external_killer.py b/scripts/drmaa_external_killer.py
index e7c53b18df05..f07d5477c421 100755
--- a/scripts/drmaa_external_killer.py
+++ b/scripts/drmaa_external_killer.py
@@ -14,7 +14,7 @@
 
 def validate_paramters():
     if len(sys.argv) < 3:
-        sys.stderr.write("usage: %s [job ID] [user uid]\n" % sys.argv[0])
+        sys.stderr.write(f"usage: {sys.argv[0]} [job ID] [user uid]\n")
         exit(1)
 
     jobID = sys.argv[1]
diff --git a/scripts/drmaa_external_runner.py b/scripts/drmaa_external_runner.py
index eba22c466efb..c07e164721a9 100755
--- a/scripts/drmaa_external_runner.py
+++ b/scripts/drmaa_external_runner.py
@@ -50,14 +50,14 @@ def get_user_id_by_name(username):
     try:
         pw = pwd.getpwnam(username)
     except KeyError:
-        sys.stderr.write("error: User name (%s) is not valid.\n" % username)
+        sys.stderr.write(f"error: User name ({username}) is not valid.\n")
         exit(1)
     return pw.pw_uid
 
 
 def json_file_exists(json_filename):
     if not os.path.exists(json_filename):
-        sys.stderr.write("error: JobTemplate file (%s) doesn't exist\n" % (json_filename))
+        sys.stderr.write(f"error: JobTemplate file ({json_filename}) doesn't exist\n")
         exit(1)
 
     return True
@@ -70,7 +70,7 @@ def validate_paramters():
         sys.argv.remove("--assign_all_groups")
 
     if len(sys.argv) < 3:
-        sys.stderr.write("usage: %s [USER-ID] [JSON-JOB-TEMPLATE-FILE]\n" % sys.argv[0])
+        sys.stderr.write(f"usage: {sys.argv[0]} [USER-ID] [JSON-JOB-TEMPLATE-FILE]\n")
         exit(1)
 
     userid = sys.argv[1]
diff --git a/scripts/dump_library_paths.py b/scripts/dump_library_paths.py
index 504b348eb2fa..4f0aacc04548 100644
--- a/scripts/dump_library_paths.py
+++ b/scripts/dump_library_paths.py
@@ -138,11 +138,11 @@ def _get_library_dataset_paths(args, kwargs):
         filename = object_store.get_filename(dataset)
         files_dir = dataset.get_extra_files_path()
         if (args.exists and object_store.exists(dataset)) or not args.exists:
-            output.write("%s\n" % _path(filename, args))
+            output.write(f"{_path(filename, args)}\n")
         elif args.exists:
             log.warning("Missing %s", filename)
         if files_dir and os.path.exists(files_dir):
-            output.write("%s\n" % _path(files_dir, args))
+            output.write(f"{_path(files_dir, args)}\n")
         last_library = library
     output.close()
 
diff --git a/scripts/external_chown_script.py b/scripts/external_chown_script.py
index 2032e5dd90cb..a08116b94a48 100755
--- a/scripts/external_chown_script.py
+++ b/scripts/external_chown_script.py
@@ -15,7 +15,7 @@
 
 def validate_parameters():
     if len(sys.argv) < 4:
-        sys.stderr.write("usage: %s path user_name gid\n" % sys.argv[0])
+        sys.stderr.write(f"usage: {sys.argv[0]} path user_name gid\n")
         exit(1)
 
     path = os.path.abspath(sys.argv[1])
@@ -28,7 +28,7 @@ def validate_parameters():
                 allowed = True
                 break
     if not allowed:
-        sys.stderr.write("owner and group modifications in %s are not allowed\n" % path)
+        sys.stderr.write(f"owner and group modifications in {path} are not allowed\n")
         sys.exit(1)
 
     galaxy_user_name = sys.argv[2]
@@ -44,7 +44,7 @@ def main():
         (stdoutdata, stderrdata) = p.communicate()
         exitcode = p.returncode
         if exitcode != 0:
-            sys.exit("external_chown_script: could not chown\ncmd was %s\n" % " ".join(cmd))
+            sys.exit("external_chown_script: could not chown\ncmd was {}\n".format(" ".join(cmd)))
 
 
 if __name__ == "__main__":
diff --git a/scripts/grt/export.py b/scripts/grt/export.py
index c5e15276b98e..aaa0da2d502d 100644
--- a/scripts/grt/export.py
+++ b/scripts/grt/export.py
@@ -56,7 +56,7 @@ def kw_metrics(job):
 
 def round_to_2sd(number):
     if number:
-        return str(int(float("%.2g" % number)))
+        return str(int(float(f"{number:.2g}")))
     else:
         return "-1"
 
diff --git a/scripts/loc_files/create_all_fasta_loc.py b/scripts/loc_files/create_all_fasta_loc.py
index e785b01509ce..cf891e081ac2 100644
--- a/scripts/loc_files/create_all_fasta_loc.py
+++ b/scripts/loc_files/create_all_fasta_loc.py
@@ -272,16 +272,16 @@ def __main__():
         paths_to_look_in = [os.path.join(options.genome_dir, "%s")]
 
     # say what we're looking in
-    print("\nLooking in:\n\t%s" % "\n\t".join(p % "<build_name>" for p in paths_to_look_in))
-    poss_names = ["<build_name>%s" % _ for _ in variants]
-    print("for files that are named %s" % ", ".join(poss_names[:-1]), end=" ")
+    print("\nLooking in:\n\t{}".format("\n\t".join(p % "<build_name>" for p in paths_to_look_in)))
+    poss_names = [f"<build_name>{_}" for _ in variants]
+    print("for files that are named {}".format(", ".join(poss_names[:-1])), end=" ")
     if len(poss_names) > 1:
-        print("or %s" % poss_names[-1], end=" ")
+        print(f"or {poss_names[-1]}", end=" ")
     if len(options.fasta_exts) == 1:
-        print("with the extension %s." % ", ".join(fasta_exts[:-1]))
+        print("with the extension {}.".format(", ".join(fasta_exts[:-1])))
     else:
         print("with the extension {} or {}.".format(", ".join(fasta_exts[:-1]), fasta_exts[-1]))
-    print("\nSkipping the following:\n\t%s" % "\n\t".join(exemptions))
+    print("\nSkipping the following:\n\t{}".format("\n\t".join(exemptions)))
 
     # get column names
     col_values = []
@@ -350,40 +350,33 @@ def __main__():
 
     # output results
     print(
-        "\nThere were %s fasta files found that were not included because they did not have the expected file names."
-        % len(unmatching_fasta_paths)
+        f"\nThere were {len(unmatching_fasta_paths)} fasta files found that were not included because they did not have the expected file names."
     )
-    print("%s fasta files were found and listed.\n" % len(fasta_locs.keys()))
+    print(f"{len(fasta_locs.keys())} fasta files were found and listed.\n")
 
     # output unmatching fasta files
     if options.unmatching_fasta and unmatching_fasta_paths:
-        open(options.unmatching_fasta, "wb").write("%s\n" % "\n".join(unmatching_fasta_paths))
+        open(options.unmatching_fasta, "wb").write("{}\n".format("\n".join(unmatching_fasta_paths)))
 
     # output loc file
-    if options.append:
-        all_fasta_loc = open(loc_path, "ab")
-    else:
-        all_fasta_loc = open(loc_path, "wb")
-    # put sample loc file text at top of file if appropriate
-    if sample_text:
-        if options.loc_sample_name:
-            all_fasta_loc.write("%s\n" % open(options.loc_sample_name, "rb").read().strip())
-        else:
-            all_fasta_loc.write("%s\n" % open("%s.sample" % loc_path, "rb").read().strip())
-    # output list of fasta files in alphabetical order
-    fasta_bases = list(fasta_locs.keys())
-    fasta_bases.sort(key=str.upper)
-    for fb in fasta_bases:
-        out_line = []
-        for col in col_values:
-            try:
-                out_line.append(fasta_locs[fb][col])
-            except KeyError:
-                raise Exception("Unexpected column (%s) encountered" % col)
-        if out_line:
-            all_fasta_loc.write("%s\n" % "\t".join(out_line))
-    # close up output loc file
-    all_fasta_loc.close()
+    with open(loc_path, "ab" if options.append else "wb") as all_fasta_loc:
+        # put sample loc file text at top of file if appropriate
+        if sample_text:
+            loc_sample_name = options.loc_sample_name if options.loc_sample_name else f"{loc_path}.sample"
+            with open(loc_sample_name, "rb") as loc_sample_name_fh:
+                all_fasta_loc.write(f"{loc_sample_name_fh.read().strip()}\n")
+        # output list of fasta files in alphabetical order
+        fasta_bases = list(fasta_locs.keys())
+        fasta_bases.sort(key=str.upper)
+        for fb in fasta_bases:
+            out_line = []
+            for col in col_values:
+                try:
+                    out_line.append(fasta_locs[fb][col])
+                except KeyError:
+                    raise Exception(f"Unexpected column ({col}) encountered")
+            if out_line:
+                all_fasta_loc.write("{}\n".format("\t".join(out_line)))
 
 
 if __name__ == "__main__":
diff --git a/scripts/microbes/create_bacteria_loc_file.py b/scripts/microbes/create_bacteria_loc_file.py
index f9dae93dbd1e..ea12b7cb57ee 100644
--- a/scripts/microbes/create_bacteria_loc_file.py
+++ b/scripts/microbes/create_bacteria_loc_file.py
@@ -95,11 +95,11 @@ def __main__():
                     chr["chromosome"],
                     "sequence",
                     "fasta",
-                    os.path.join(org["base_dir"], "%s.fna" % chr["chromosome"]),
+                    os.path.join(org["base_dir"], f"{chr['chromosome']}.fna"),
                 )
             )
             # GeneMark
-            if os.path.exists(os.path.join(org["base_dir"], "%s.GeneMark.bed" % chr["chromosome"])):
+            if os.path.exists(os.path.join(org["base_dir"], f"{chr['chromosome']}.GeneMark.bed")):
                 print(
                     "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
                         build,
@@ -109,11 +109,11 @@ def __main__():
                         chr["chromosome"],
                         "GeneMark",
                         "bed",
-                        os.path.join(org["base_dir"], "%s.GeneMark.bed" % chr["chromosome"]),
+                        os.path.join(org["base_dir"], f"{chr['chromosome']}.GeneMark.bed"),
                     )
                 )
             # GenMarkHMM
-            if os.path.exists(os.path.join(org["base_dir"], "%s.GeneMarkHMM.bed" % chr["chromosome"])):
+            if os.path.exists(os.path.join(org["base_dir"], f"{chr['chromosome']}.GeneMarkHMM.bed")):
                 print(
                     "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
                         build,
@@ -123,11 +123,11 @@ def __main__():
                         chr["chromosome"],
                         "GeneMarkHMM",
                         "bed",
-                        os.path.join(org["base_dir"], "%s.GeneMarkHMM.bed" % chr["chromosome"]),
+                        os.path.join(org["base_dir"], f"{chr['chromosome']}.GeneMarkHMM.bed"),
                     )
                 )
             # Glimmer3
-            if os.path.exists(os.path.join(org["base_dir"], "%s.Glimmer3.bed" % chr["chromosome"])):
+            if os.path.exists(os.path.join(org["base_dir"], f"{chr['chromosome']}.Glimmer3.bed")):
                 print(
                     "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
                         build,
@@ -137,7 +137,7 @@ def __main__():
                         chr["chromosome"],
                         "Glimmer3",
                         "bed",
-                        os.path.join(org["base_dir"], "%s.Glimmer3.bed" % chr["chromosome"]),
+                        os.path.join(org["base_dir"], f"{chr['chromosome']}.Glimmer3.bed"),
                     )
                 )
 
diff --git a/scripts/microbes/create_nib_seq_loc_file.py b/scripts/microbes/create_nib_seq_loc_file.py
index 3a79d9b84e5d..1ced877e34de 100644
--- a/scripts/microbes/create_nib_seq_loc_file.py
+++ b/scripts/microbes/create_nib_seq_loc_file.py
@@ -74,8 +74,8 @@ def __main__():
         for chr in org["chrs"]:
             chr = org["chrs"][chr]
 
-            fasta_file = os.path.join(org["base_dir"], "%s.fna" % chr["chromosome"])
-            nib_out_file = os.path.join(seq_path, "%s.nib " % chr["chromosome"])
+            fasta_file = os.path.join(org["base_dir"], f"{chr['chromosome']}.fna")
+            nib_out_file = os.path.join(seq_path, f"{chr['chromosome']}.nib ")
             # create nibs using faToNib binary
             # TODO: when bx supports writing nib, use it here instead
             command = f"faToNib {fasta_file} {nib_out_file}"
diff --git a/scripts/microbes/harvest_bacteria.py b/scripts/microbes/harvest_bacteria.py
index a94ae088dbae..89a4b59df51e 100644
--- a/scripts/microbes/harvest_bacteria.py
+++ b/scripts/microbes/harvest_bacteria.py
@@ -158,18 +158,18 @@ def process_FASTA(filename, org_num, refseq):
     fasta = "".join(fasta)
 
     # Create Chrom Info File:
-    chrom_info_file = open(os.path.join(os.path.split(filename)[0], "%s.info" % refseq), "wb+")
+    chrom_info_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.info"), "wb+")
     chrom_info_file.write(f"chromosome={refseq}\nname={chr_name}\nlength={len(fasta)}\norganism={org_num}\n")
     try:
-        chrom_info_file.write("gi=%s\n" % accesions["gi"])
+        chrom_info_file.write(f"gi={accesions['gi']}\n")
     except Exception:
         chrom_info_file.write("gi=None\n")
     try:
-        chrom_info_file.write("gb=%s\n" % accesions["gb"])
+        chrom_info_file.write(f"gb={accesions['gb']}\n")
     except Exception:
         chrom_info_file.write("gb=None\n")
     try:
-        chrom_info_file.write("refseq=%s\n" % refseq)
+        chrom_info_file.write(f"refseq={refseq}\n")
     except Exception:
         chrom_info_file.write("refseq=None\n")
     chrom_info_file.close()
@@ -191,7 +191,7 @@ def process_Glimmer3(filename, org_num, refseq):
     except Exception as e:
         print("Converting Glimmer3 to bed FAILED! For chrom:", refseq, "file:", filename, e)
         glimmer3_bed = []
-    glimmer3_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.Glimmer3.bed" % refseq), "wb+")
+    glimmer3_bed_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.Glimmer3.bed"), "wb+")
     glimmer3_bed_file.write("\n".join(glimmer3_bed))
     glimmer3_bed_file.close()
 
@@ -202,7 +202,7 @@ def process_GeneMarkHMM(filename, org_num, refseq):
     except Exception as e:
         print("Converting GeneMarkHMM to bed FAILED! For chrom:", refseq, "file:", filename, e)
         geneMarkHMM_bed = []
-    geneMarkHMM_bed_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.GeneMarkHMM.bed" % refseq), "wb+")
+    geneMarkHMM_bed_bed_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.GeneMarkHMM.bed"), "wb+")
     geneMarkHMM_bed_bed_file.write("\n".join(geneMarkHMM_bed))
     geneMarkHMM_bed_bed_file.close()
 
@@ -213,7 +213,7 @@ def process_GeneMark(filename, org_num, refseq):
     except Exception as e:
         print("Converting GeneMark to bed FAILED! For chrom:", refseq, "file:", filename, e)
         geneMark_bed = []
-    geneMark_bed_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.GeneMark.bed" % refseq), "wb+")
+    geneMark_bed_bed_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.GeneMark.bed"), "wb+")
     geneMark_bed_bed_file.write("\n".join(geneMark_bed))
     geneMark_bed_bed_file.close()
 
@@ -228,9 +228,9 @@ def __main__():
 
     try:
         os.mkdir(base_dir)
-        print("path '%s' has been created" % base_dir)
+        print(f"path '{base_dir}' has been created")
     except Exception:
-        print("path '%s' seems to already exist" % base_dir)
+        print(f"path '{base_dir}' seems to already exist")
 
     for org_num, name, chroms, kingdom, group, _, _, info_url, ftp_url in iter_genome_projects():
         if chroms is None:
@@ -240,7 +240,7 @@ def __main__():
             org_dir = os.path.join(base_dir, org_num)
             os.mkdir(org_dir)
         except Exception:
-            print("Organism %s already exists on disk, skipping" % org_num)
+            print(f"Organism {org_num} already exists on disk, skipping")
             continue
 
         # get ftp contents
@@ -254,14 +254,14 @@ def __main__():
                 print("Org:", org_num, "chrom:", refseq, "[", time.time() - start_time, "seconds elapsed. ]")
 
         # Create org info file
-        info_file = open(os.path.join(org_dir, "%s.info" % org_num), "wb+")
-        info_file.write("genome project id=%s\n" % org_num)
-        info_file.write("name=%s\n" % name)
-        info_file.write("kingdom=%s\n" % kingdom)
-        info_file.write("group=%s\n" % group)
-        info_file.write("chromosomes=%s\n" % ",".join(chroms))
-        info_file.write("info url=%s\n" % info_url)
-        info_file.write("ftp url=%s\n" % ftp_url)
+        info_file = open(os.path.join(org_dir, f"{org_num}.info"), "wb+")
+        info_file.write(f"genome project id={org_num}\n")
+        info_file.write(f"name={name}\n")
+        info_file.write(f"kingdom={kingdom}\n")
+        info_file.write(f"group={group}\n")
+        info_file.write("chromosomes={}\n".format(",".join(chroms)))
+        info_file.write(f"info url={info_url}\n")
+        info_file.write(f"ftp url={ftp_url}\n")
         info_file.close()
 
     print("Finished Harvesting", "[", time.time() - start_time, "seconds elapsed. ]")
diff --git a/scripts/pages_identifier_conversion.py b/scripts/pages_identifier_conversion.py
index b290206ecbe8..8aaee5f2247c 100644
--- a/scripts/pages_identifier_conversion.py
+++ b/scripts/pages_identifier_conversion.py
@@ -58,11 +58,11 @@ def main(argv):
                     with transaction(session):
                         session.commit()
                 else:
-                    print("Modifying revision %s." % p.id)
+                    print(f"Modifying revision {p.id}.")
                     print(difflib.unified_diff(p.content, newcontent))
         except Exception:
             logging.exception(
-                "Error parsing page, rolling changes back and skipping revision %s.  Please report this error." % p.id
+                "Error parsing page, rolling changes back and skipping revision %s.  Please report this error.", p.id
             )
             session.rollback()
 
diff --git a/scripts/runtime_stats.py b/scripts/runtime_stats.py
index dd11460a2f0e..9e6c9e5277aa 100755
--- a/scripts/runtime_stats.py
+++ b/scripts/runtime_stats.py
@@ -90,7 +90,7 @@ def parse_arguments():
     parser.add_argument("-M", "--max", type=int, default=-1, help="Ignore runtimes greater than MAX seconds")
     parser.add_argument("-u", "--user", help="Return stats for only this user (id, email, " "or username)")
     parser.add_argument(
-        "-s", "--source", default="metrics", help="Runtime data source (SOURCES: %s)" % ", ".join(DATA_SOURCES)
+        "-s", "--source", default="metrics", help="Runtime data source (SOURCES: {})".format(", ".join(DATA_SOURCES))
     )
     args = parser.parse_args()
 
@@ -144,13 +144,13 @@ def query(
             if row:
                 user_id = row[0]
             else:
-                print("Invalid user: %s" % user)
+                print(f"Invalid user: {user}")
                 sys.exit(1)
 
     if like:
-        query_tool_id = "%%/%s/%%" % tool_id
+        query_tool_id = f"%/{tool_id}/%"
     elif "/" in tool_id and not re.match(r"\d+\.\d+", tool_id.split("/")[-1]):
-        query_tool_id = "%s%%" % tool_id
+        query_tool_id = f"{tool_id}%"
         like = True
     else:
         query_tool_id = tool_id
@@ -187,14 +187,14 @@ def query(
         if min > 0 and max > 0:
             time_clause = """WHERE ctimes[1] - ctimes[2] > interval %s
           AND ctimes[1] - ctimes[2] < interval %s"""
-            sql_args.append("%s seconds" % min)
-            sql_args.append("%s seconds" % max)
+            sql_args.append(f"{min} seconds")
+            sql_args.append(f"{max} seconds")
         elif min > 0:
             time_clause = "WHERE ctimes[1] - ctimes[2] > interval %s"
-            sql_args.append("%s seconds" % min)
+            sql_args.append(f"{min} seconds")
         elif max > 0:
             time_clause = "WHERE ctimes[1] - ctimes[2] < interval %s"
-            sql_args.append("%s seconds" % max)
+            sql_args.append(f"{max} seconds")
         else:
             time_clause = ""
         sql = HISTORY_SQL
@@ -218,7 +218,7 @@ def query(
         return
 
     if user:
-        print("Displaying statistics for user %s" % user)
+        print(f"Displaying statistics for user {user}")
 
     stats = (
         ("Mean runtime", numpy.mean(times)),
@@ -229,11 +229,11 @@ def query(
 
     for name, seconds in stats:
         hours, minutes = nice_times(seconds)
-        msg = name + " is %0.0f seconds" % seconds
+        msg = name + f" is {seconds:0.0f} seconds"
         if minutes:
-            msg += " (=%0.2f minutes)" % minutes
+            msg += f" (={minutes:0.2f} minutes)"
         if hours:
-            msg += " (=%0.2f hours)" % hours
+            msg += f" (={hours:0.2f} hours)"
         print(msg)
 
 
diff --git a/scripts/set_user_disk_usage.py b/scripts/set_user_disk_usage.py
index b23b159b0ca8..9c10d3c8f554 100755
--- a/scripts/set_user_disk_usage.py
+++ b/scripts/set_user_disk_usage.py
@@ -62,9 +62,9 @@ def quotacheck(sa_session, users, engine, object_store):
         print("none")
     else:
         if new > current:
-            print("+%s" % (nice_size(new - current)))
+            print(f"+{nice_size(new - current)}")
         else:
-            print("-%s" % (nice_size(current - new)))
+            print(f"-{nice_size(current - new)}")
 
 
 if __name__ == "__main__":
diff --git a/scripts/tests_markdown.py b/scripts/tests_markdown.py
index 1b6fb8edd2c4..1fc53003affd 100644
--- a/scripts/tests_markdown.py
+++ b/scripts/tests_markdown.py
@@ -244,10 +244,10 @@ def summarize_counter(c):
             continue
 
         endpoint_summary = {"total_time": summarize_times(timings), "label": endpoint[len("api.") :]}
-        sql_times = "sql.%s" % endpoint
+        sql_times = f"sql.{endpoint}"
         if sql_times in timing:
             endpoint_summary["sql_time"] = summarize_times(timing[sql_times])
-        sql_queries = "sqlqueries.%s" % endpoint
+        sql_queries = f"sqlqueries.{endpoint}"
         if sql_queries in counter:
             endpoint_summary["sql_queries"] = summarize_counter(counter[sql_queries])
         api_endpoints[endpoint] = endpoint_summary
diff --git a/scripts/tool_shed/api/common.py b/scripts/tool_shed/api/common.py
index 16ad847ec524..fb1ec34bba2f 100644
--- a/scripts/tool_shed/api/common.py
+++ b/scripts/tool_shed/api/common.py
@@ -35,7 +35,7 @@ def display(url, api_key=None, return_formatted=True):
             if "url" in i:
                 print("#%d: %s" % (n + 1, i.pop("url")))
             if "name" in i:
-                print("  name: %s" % i.pop("name"))
+                print(f"  name: {i.pop('name')}")
             for k, v in i.items():
                 print(f"  {k}: {v}")
         print()
@@ -47,7 +47,7 @@ def display(url, api_key=None, return_formatted=True):
         for k, v in r.items():
             print(f"{k}: {v}")
     else:
-        print("response is unknown type: %s" % type(r))
+        print(f"response is unknown type: {type(r)}")
 
 
 def get(url, api_key=None):
@@ -100,7 +100,7 @@ def submit(url, data, api_key=None, return_formatted=True):
                 else:
                     print("----")
                 if "name" in i:
-                    print("  name: %s" % i.pop("name"))
+                    print(f"  name: {i.pop('name')}")
                 for k, v in i.items():
                     print(f"  {k}: {v}")
             else:
diff --git a/scripts/tool_shed/api/create_categories.py b/scripts/tool_shed/api/create_categories.py
index 86c76a1200f8..6f6a7a5a3389 100644
--- a/scripts/tool_shed/api/create_categories.py
+++ b/scripts/tool_shed/api/create_categories.py
@@ -31,7 +31,7 @@ def main(options):
     from_tool_shed = options.from_tool_shed.rstrip("/")
     to_tool_shed = options.to_tool_shed.rstrip("/")
     # Get the categories from the specified Tool Shed.
-    url = "%s/api/categories" % from_tool_shed
+    url = f"{from_tool_shed}/api/categories"
     category_dicts = get(url)
     create_response_dicts = []
     for category_dict in category_dicts:
@@ -39,7 +39,7 @@ def main(options):
         description = category_dict.get("description", None)
         if name is not None and description is not None:
             data = dict(name=name, description=description)
-            url = "%s/api/categories" % to_tool_shed
+            url = f"{to_tool_shed}/api/categories"
             try:
                 response = submit(url, data, api_key)
             except Exception as e:
diff --git a/scripts/tool_shed/api/create_users.py b/scripts/tool_shed/api/create_users.py
index dea8adef38fc..5a6e3f7fa860 100644
--- a/scripts/tool_shed/api/create_users.py
+++ b/scripts/tool_shed/api/create_users.py
@@ -32,16 +32,16 @@ def main(options):
     from_tool_shed = options.from_tool_shed.rstrip("/")
     to_tool_shed = options.to_tool_shed.rstrip("/")
     # Get the users from the specified Tool Shed.
-    url = "%s/api/users" % from_tool_shed
+    url = f"{from_tool_shed}/api/users"
     user_dicts = get(url)
     create_response_dicts = []
     for user_dict in user_dicts:
         username = user_dict.get("username", None)
         if username is not None:
-            email = "%s@test.org" % username
+            email = f"{username}@test.org"
             password = "testuser"
             data = dict(email=email, password=password, username=username)
-            url = "%s/api/users" % to_tool_shed
+            url = f"{to_tool_shed}/api/users"
             try:
                 response = submit(url, data, api_key)
             except Exception as e:
diff --git a/scripts/tool_shed/deprecate_repositories_without_metadata.py b/scripts/tool_shed/deprecate_repositories_without_metadata.py
index beddab51dbd0..6ab395d0354b 100644
--- a/scripts/tool_shed/deprecate_repositories_without_metadata.py
+++ b/scripts/tool_shed/deprecate_repositories_without_metadata.py
@@ -68,7 +68,7 @@ def main():
     try:
         ini_file = args[0]
     except IndexError:
-        sys.exit("Usage: python %s <tool shed .ini file> [options]" % sys.argv[0])
+        sys.exit(f"Usage: python {sys.argv[0]} <tool shed .ini file> [options]")
     config_parser = configparser.ConfigParser({"here": os.getcwd()})
     config_parser.read(ini_file)
     config_dict = {}
@@ -103,7 +103,7 @@ def send_mail_to_owner(app, owner, email, repositories_deprecated, days=14):
     elif url is None:
         print("# Environment variable TOOL_SHED_CANONICAL_URL not set, not sending email to repository owner.")
         return
-    subject = "Regarding your tool shed repositories at %s" % url
+    subject = f"Regarding your tool shed repositories at {url}"
     message_body_template = (
         "The tool shed automated repository checker has discovered that one or more of your repositories hosted "
         + "at this tool shed url ${url} have remained empty for over ${days} days, so they have been marked as deprecated. If you have plans "
@@ -123,7 +123,7 @@ def send_mail_to_owner(app, owner, email, repositories_deprecated, days=14):
         )
         return True
     except Exception as e:
-        print("# An error occurred attempting to send email: %s" % e)
+        print(f"# An error occurred attempting to send email: {e}")
         return False
 
 
@@ -193,7 +193,7 @@ class DeprecateRepositoriesApplication:
 
     def __init__(self, config):
         if config.database_connection is False:
-            config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % config.database
+            config.database_connection = f"sqlite:///{config.database}?isolation_level=IMMEDIATE"
         # Setup the database engine and ORM
         self.model = tool_shed.webapp.model.mapping.init(
             config.file_path, config.database_connection, engine_options={}, create_tables=False
diff --git a/scripts/tools/re_escape_output.py b/scripts/tools/re_escape_output.py
index 9deab8c743cf..0ec3ee1e1edc 100644
--- a/scripts/tools/re_escape_output.py
+++ b/scripts/tools/re_escape_output.py
@@ -27,7 +27,7 @@ def __main__():
     if options.multiline:
         lines = [re.escape(input.read())]
     else:
-        lines = ["%s\n" % re.escape(line.rstrip("\n\r")) for line in input]
+        lines = ["{}\n".format(re.escape(line.rstrip("\n\r"))) for line in input]
     output.writelines(lines)
     output.close()
 
diff --git a/scripts/update_shed_config_path.py b/scripts/update_shed_config_path.py
index d3619a099704..a5bee3af9f63 100644
--- a/scripts/update_shed_config_path.py
+++ b/scripts/update_shed_config_path.py
@@ -40,7 +40,7 @@ def create_database(config_file):
     if database_connection is None:
         database_connection = parser.get("app:main", "database_connection")
     if database_connection is None:
-        database_connection = "sqlite:///%s" % parser.get("app:main", "database_file")
+        database_connection = "sqlite:///{}".format(parser.get("app:main", "database_file"))
     if database_connection is None:
         print("Unable to determine correct database connection.")
         exit(1)
@@ -78,7 +78,7 @@ def create_database(config_file):
     )
     opts = parser.parse_args()
     if not os.path.exists(opts.good_filename) and not opts.force:
-        print("The file %s does not exist, use the --force option to proceed." % opts.good_filename)
+        print(f"The file {opts.good_filename} does not exist, use the --force option to proceed.")
         exit(1)
     session, model = create_database(opts.config_file)
     exit(main(opts, session, model))
diff --git a/test/integration/chained_dyndest_rules/module2/rules.py b/test/integration/chained_dyndest_rules/module2/rules.py
index 1d7ea5c6eab3..b3b0c8048de6 100644
--- a/test/integration/chained_dyndest_rules/module2/rules.py
+++ b/test/integration/chained_dyndest_rules/module2/rules.py
@@ -15,7 +15,7 @@ def dyndest_chain_2(tmp_dir_prefix):
             "type": "python",
             "function": "dyndest_chain_3",
             "rules_module": "integration.chained_dyndest_rules.module3",
-            "tmp_dir_prefix_two": "%sand2" % tmp_dir_prefix,
+            "tmp_dir_prefix_two": f"{tmp_dir_prefix}and2",
         },
     )
 
diff --git a/test/integration/chained_dyndest_rules/module3/rules.py b/test/integration/chained_dyndest_rules/module3/rules.py
index f329428f24ef..add61a941ac0 100644
--- a/test/integration/chained_dyndest_rules/module3/rules.py
+++ b/test/integration/chained_dyndest_rules/module3/rules.py
@@ -14,5 +14,5 @@ def dyndest_chain_2():
 
 
 def dyndest_chain_3(tmp_dir_prefix_two):
-    tmp_dir = "$(mktemp -d -p $(pwd) %sand3XXXXXXXXXXXX)" % tmp_dir_prefix_two
+    tmp_dir = f"$(mktemp -d -p $(pwd) {tmp_dir_prefix_two}and3XXXXXXXXXXXX)"
     return JobDestination(runner="local", params={"tmp_dir": tmp_dir})
diff --git a/test/integration/test_repository_operations.py b/test/integration/test_repository_operations.py
index 551d3a24125d..510067db9660 100644
--- a/test/integration/test_repository_operations.py
+++ b/test/integration/test_repository_operations.py
@@ -66,7 +66,7 @@ def test_repository_update(self):
         response = self._install_repository(revision=REVISION_4, version="0.0.3", allow_upgraded=True)[0]
         assert int(response["ctx_rev"]) >= 4
         latest_revision = response["changeset_revision"]
-        repo_response = self._get("/api/tool_shed_repositories/%s" % response["id"]).json()
+        repo_response = self._get(f"/api/tool_shed_repositories/{response['id']}").json()
         assert repo_response["tool_shed_status"]["revision_update"] == "False"  # that should really be a boolean
         # now checkout revision 3 and attempt an update
         path_components = [
@@ -104,7 +104,7 @@ def test_repository_update(self):
             shed_config.write(shed_text)
         self._get("/api/tool_shed_repositories/check_for_updates", data={"id": response["id"]}, admin=True).json()
         # At this point things should look like there is minor update available
-        repo_response = self._get("/api/tool_shed_repositories/%s" % response["id"])
+        repo_response = self._get(f"/api/tool_shed_repositories/{response['id']}")
         repo_response.raise_for_status()
         repo_json = repo_response.json()
         assert repo_json["tool_shed_status"]["revision_update"] == "True"
diff --git a/test/integration/test_structured_dataset.py b/test/integration/test_structured_dataset.py
index ba81c3365cef..4f21261aaefa 100644
--- a/test/integration/test_structured_dataset.py
+++ b/test/integration/test_structured_dataset.py
@@ -25,7 +25,7 @@ def setUp(self):
 
     def test_fail_on_nonbinary(self):
         dataset = self.dataset_populator.new_dataset(
-            self.test_history_id, "file://%s/random-file" % TEST_DATA_DIRECTORY, file_type="txt", wait=True
+            self.test_history_id, f"file://{TEST_DATA_DIRECTORY}/random-file", file_type="txt", wait=True
         )
         dataset_id = dataset["dataset_id"]
         response = self._get(f"datasets/{dataset_id}/content/meta")
@@ -33,7 +33,7 @@ def test_fail_on_nonbinary(self):
 
     def test_api_meta(self):
         dataset = self.dataset_populator.new_dataset(
-            self.test_history_id, "file://%s/chopper.h5" % TEST_DATA_DIRECTORY, file_type="h5", wait=True
+            self.test_history_id, f"file://{TEST_DATA_DIRECTORY}/chopper.h5", file_type="h5", wait=True
         )
         dataset_id = dataset["dataset_id"]
         response = self._get(f"datasets/{dataset_id}/content/meta")
@@ -43,7 +43,7 @@ def test_api_meta(self):
 
     def test_api_attr(self):
         dataset = self.dataset_populator.new_dataset(
-            self.test_history_id, "file://%s/chopper.h5" % TEST_DATA_DIRECTORY, file_type="h5", wait=True
+            self.test_history_id, f"file://{TEST_DATA_DIRECTORY}/chopper.h5", file_type="h5", wait=True
         )
         dataset_id = dataset["dataset_id"]
         response = self._get(f"datasets/{dataset_id}/content/attr")
@@ -53,7 +53,7 @@ def test_api_attr(self):
 
     def test_api_stats(self):
         dataset = self.dataset_populator.new_dataset(
-            self.test_history_id, "file://%s/chopper.h5" % TEST_DATA_DIRECTORY, file_type="h5", wait=True
+            self.test_history_id, f"file://{TEST_DATA_DIRECTORY}/chopper.h5", file_type="h5", wait=True
         )
         dataset_id = dataset["dataset_id"]
         response = self._get(f"datasets/{dataset_id}/content/stats?path=%2Fentry%2Fdata%2Fdata")
@@ -63,7 +63,7 @@ def test_api_stats(self):
 
     def test_api_data(self):
         dataset = self.dataset_populator.new_dataset(
-            self.test_history_id, "file://%s/chopper.h5" % TEST_DATA_DIRECTORY, file_type="h5", wait=True
+            self.test_history_id, f"file://{TEST_DATA_DIRECTORY}/chopper.h5", file_type="h5", wait=True
         )
         dataset_id = dataset["dataset_id"]
         response = self._get(f"datasets/{dataset_id}/content/data?path=%2Fentry%2Fdata%2Fdata")
diff --git a/test/manual/gen_history_export_test_artifacts.py b/test/manual/gen_history_export_test_artifacts.py
index 1d971678e3a3..6840f2615676 100644
--- a/test/manual/gen_history_export_test_artifacts.py
+++ b/test/manual/gen_history_export_test_artifacts.py
@@ -49,7 +49,7 @@ def _gi(args):
     gi = galaxy.GalaxyInstance(args.host, key=args.api_key)
     name = "histexport-user-%d" % random.randint(0, 1000000)
 
-    user = gi.users.create_local_user(name, "%s@galaxytesting.dev" % name, "pass123")
+    user = gi.users.create_local_user(name, f"{name}@galaxytesting.dev", "pass123")
     user_id = user["id"]
     api_key = gi.users.create_user_apikey(user_id)
     user_gi = galaxy.GalaxyInstance(args.host, api_key)
diff --git a/test/manual/workflows_scaling.py b/test/manual/workflows_scaling.py
index f1b88332ba5f..2a1e39413342 100644
--- a/test/manual/workflows_scaling.py
+++ b/test/manual/workflows_scaling.py
@@ -90,10 +90,10 @@ def _run(args, gi, workflow_id, uuid):
         label_map = {}
 
     workflow_request = dict(
-        history="hist_id=%s" % history_id,
+        history=f"hist_id={history_id}",
     )
     workflow_request["inputs"] = json.dumps(label_map)
-    url = "workflows/%s/usage" % (workflow_id)
+    url = f"workflows/{workflow_id}/usage"
     invoke_response = dataset_populator._post(url, data=workflow_request).json()
     invocation_id = invoke_response["id"]
     workflow_populator = GiWorkflowPopulator(gi)
@@ -174,7 +174,7 @@ def _gi(args):
     gi = galaxy.GalaxyInstance(args.host, key=args.api_key)
     name = "wftest-user-%d" % random.randint(0, 1000000)
 
-    user = gi.users.create_local_user(name, "%s@galaxytesting.dev" % name, "pass123")
+    user = gi.users.create_local_user(name, f"{name}@galaxytesting.dev", "pass123")
     user_id = user["id"]
     api_key = gi.users.create_user_apikey(user_id)
     user_gi = galaxy.GalaxyInstance(args.host, api_key)
diff --git a/test/unit/app/queue_worker/conftest.py b/test/unit/app/queue_worker/conftest.py
index 4e8fa6b0be4f..728d91460237 100644
--- a/test/unit/app/queue_worker/conftest.py
+++ b/test/unit/app/queue_worker/conftest.py
@@ -20,7 +20,7 @@
 def create_base_test(connection, amqp_type: str, amqp_connection: Optional[str] = None):
     app = galaxy_mock.MockApp(database_connection=connection)
     app.config.database_connection = connection
-    app.config.amqp_internal_connection = amqp_connection or "sqlalchemy+%s" % app.config.database_connection
+    app.config.amqp_internal_connection = amqp_connection or f"sqlalchemy+{app.config.database_connection}"
     app.amqp_type = amqp_type
     return app
 
diff --git a/test/unit/app/test_markdown_validate.py b/test/unit/app/test_markdown_validate.py
index a1fbb0487112..0c99276ff915 100644
--- a/test/unit/app/test_markdown_validate.py
+++ b/test/unit/app/test_markdown_validate.py
@@ -13,7 +13,7 @@ def assert_markdown_invalid(markdown, at_line=None):
         failed = True
         if at_line is not None:
             assert "Invalid line %d" % (at_line + 1) in str(e)
-    assert failed, "Expected markdown [%s] to fail validation but it did not." % markdown
+    assert failed, f"Expected markdown [{markdown}] to fail validation but it did not."
 
 
 def test_markdown_validation():
diff --git a/test/unit/app/tools/conftest.py b/test/unit/app/tools/conftest.py
index ca09a3bc5514..f69d6ea70bff 100644
--- a/test/unit/app/tools/conftest.py
+++ b/test/unit/app/tools/conftest.py
@@ -56,7 +56,7 @@ def create_repo(session, changeset, installed_changeset, config_filename=None):
         "tools": [
             {
                 "add_to_tool_panel": False,  # to have repository.includes_tools_for_display_in_tool_panel=False in InstalledRepositoryManager.activate_repository()
-                "guid": "github.com/galaxyproject/example/test_tool/0.%s" % changeset,
+                "guid": f"github.com/galaxyproject/example/test_tool/0.{changeset}",
                 "tool_config": "tool.xml",
             }
         ],
diff --git a/test/unit/app/tools/test_wrappers.py b/test/unit/app/tools/test_wrappers.py
index a7be2e271d1b..746fef91f480 100644
--- a/test/unit/app/tools/test_wrappers.py
+++ b/test/unit/app/tools/test_wrappers.py
@@ -128,17 +128,17 @@ def valuewrapper(tool, value, paramtype, optional=False):
     parameter: ToolParameter
     if paramtype == "integer":
         optional = 'optional="true"' if optional else 'value="10"'
-        parameter = IntegerToolParameter(tool, XML('<param name="blah" type="integer" %s min="0" />' % optional))
+        parameter = IntegerToolParameter(tool, XML(f'<param name="blah" type="integer" {optional} min="0" />'))
     elif paramtype == "text":
         optional = 'optional="true"' if optional else 'value="foo"'
-        parameter = TextToolParameter(tool, XML('<param name="blah" type="text" %s/>' % optional))
+        parameter = TextToolParameter(tool, XML(f'<param name="blah" type="text" {optional}/>'))
     elif paramtype == "float":
         optional = 'optional="true"' if optional else 'value="10.0"'
-        parameter = FloatToolParameter(tool, XML('<param name="blah" type="float" %s/>' % optional))
+        parameter = FloatToolParameter(tool, XML(f'<param name="blah" type="float" {optional}/>'))
     elif paramtype == "boolean":
         optional = 'optional="true"' if optional else 'value=""'
         parameter = BooleanToolParameter(
-            tool, XML('<param name="blah" type="boolean" truevalue="truevalue" falsevalue="falsevalue" %s/>' % optional)
+            tool, XML(f'<param name="blah" type="boolean" truevalue="truevalue" falsevalue="falsevalue" {optional}/>')
         )
     return InputValueWrapper(parameter, value)
 
@@ -234,7 +234,7 @@ def input_extra_files_rewrite(self, dataset):
         return self.false_extra_files_path
 
     def unstructured_path_rewrite(self, path):
-        return "Rewrite<%s>" % path
+        return f"Rewrite<{path}>"
 
 
 def test_dataset_false_extra_files_path():
@@ -287,14 +287,13 @@ def _drilldown_parameter(tool):
 def _setup_blast_tool(tool, multiple=False):
     tool.app.write_test_tool_data("blastdb.loc", "val1\tname1\tpath1\nval2\tname2\tpath2\n")
     xml = XML(
-        """<param name="database" type="select" label="Nucleotide BLAST database" multiple="%s">
+        f"""<param name="database" type="select" label="Nucleotide BLAST database" multiple="{multiple}">
         <options from_file="blastdb.loc">
             <column name="value" index="0"/>
             <column name="name" index="1"/>
             <column name="path" index="2"/>
         </options>
     </param>"""
-        % multiple
     )
     parameter = SelectToolParameter(tool, xml)
     return parameter
diff --git a/test/unit/config/test_path_resolves_to.py b/test/unit/config/test_path_resolves_to.py
index d3252147dffb..97953b3d0787 100644
--- a/test/unit/config/test_path_resolves_to.py
+++ b/test/unit/config/test_path_resolves_to.py
@@ -157,7 +157,7 @@ def test_add_sample_file(mock_init, monkeypatch):
     # - has ".sample" suffix
     # Last value (sample file) resolved and listified; others dropped as files do not exist
     monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1", "path4"})
-    monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: "/sample-dir/%s" % path)
+    monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: f"/sample-dir/{path}")
     config = BaseAppConfiguration()
 
     assert config._raw_config["path1"] == "my-config-files"
@@ -169,7 +169,7 @@ def test_add_sample_file(mock_init, monkeypatch):
 def test_select_one_path_from_list(mock_init, monkeypatch):
     # Expected: files do not exist, so use last file in list (would be sample file); value is not a list
     monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1"})
-    monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: "/sample-dir/%s" % path)
+    monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: f"/sample-dir/{path}")
     config = BaseAppConfiguration()
 
     assert config._raw_config["path1"] == "my-config-files"
@@ -227,7 +227,7 @@ def path_exists(_, path):
         return True if path == "root/foo" else False
 
     monkeypatch.setattr(BaseAppConfiguration, "_path_exists", path_exists)
-    monkeypatch.setattr(BaseAppConfiguration, "_in_root_dir", lambda _, path: "root/%s" % path)
+    monkeypatch.setattr(BaseAppConfiguration, "_in_root_dir", lambda _, path: f"root/{path}")
     monkeypatch.setattr(BaseAppConfiguration, "paths_to_check_against_root", {"path1", "path4"})
 
 
diff --git a/test/unit/data/test_model_copy.py b/test/unit/data/test_model_copy.py
index 6487442f69ca..29416b552b83 100644
--- a/test/unit/data/test_model_copy.py
+++ b/test/unit/data/test_model_copy.py
@@ -53,7 +53,7 @@ def test_history_dataset_copy(num_datasets=NUM_DATASETS, include_metadata_file=I
         session.refresh(old_history)
         new_update_time = session.get(model.History, old_history.id).update_time
         assert original_update_time == new_update_time
-        print("history copied %s" % history_copy_timer)
+        print(f"history copied {history_copy_timer}")
         assert new_history.name == "new name"
         assert new_history.user == old_history.user
         for hda in new_history.active_datasets:
@@ -121,7 +121,7 @@ def test_history_collection_copy(list_size=NUM_DATASETS):
 
         history_copy_timer = ExecutionTimer()
         new_history = old_history.copy(target_user=old_history.user)
-        print("history copied %s" % history_copy_timer)
+        print(f"history copied {history_copy_timer}")
 
         for hda in new_history.active_datasets:
             assert hda.get_size() == 3
diff --git a/test/unit/data/test_quota.py b/test/unit/data/test_quota.py
index 96187045829d..5c34ea7cb056 100644
--- a/test/unit/data/test_quota.py
+++ b/test/unit/data/test_quota.py
@@ -67,7 +67,7 @@ def test_calculate_usage_per_source(self):
 class TestCalculateUsage(BaseModelTestCase):
     def setUp(self):
         model = self.model
-        u = model.User(email="calc_usage%s@example.com" % str(uuid.uuid1()), password="password")
+        u = model.User(email=f"calc_usage{uuid.uuid1()}@example.com", password="password")
         self.persist(u)
         h = model.History(name="History for Calculated Usage", user=u)
         self.persist(h)
diff --git a/test/unit/files/test_posix.py b/test/unit/files/test_posix.py
index 579b8ee1ca60..f64322db082b 100644
--- a/test/unit/files/test_posix.py
+++ b/test/unit/files/test_posix.py
@@ -480,7 +480,7 @@ def _configured_file_sources_with_root(
     if writable is not None:
         plugin["writable"] = writable
     if per_user and root:
-        plugin["root"] = "%s/${user.username}" % root
+        plugin["root"] = f"{root}/${{user.username}}"
         # setup files just for alice
         root = os.path.join(root, "alice")
         os.mkdir(root)
diff --git a/test/unit/objectstore/test_objectstore.py b/test/unit/objectstore/test_objectstore.py
index 4956ac970834..abcb6985a16c 100644
--- a/test/unit/objectstore/test_objectstore.py
+++ b/test/unit/objectstore/test_objectstore.py
@@ -182,7 +182,7 @@ def test_disk_store_by_uuid():
                 directory.temp_directory,
                 "files1",
                 output_dataset.rel_path_for_uuid_test(),
-                "dataset_%s.dat" % output_dataset.uuid,
+                f"dataset_{output_dataset.uuid}.dat",
             )
             assert not os.path.exists(output_real_path)
             output_working_path = directory.write("NEW CONTENTS", "job_working_directory1/example_output")
diff --git a/test/unit/tool_shed/test_shed_index.py b/test/unit/tool_shed/test_shed_index.py
index b589dc74fd83..ea5d5ef1bba4 100644
--- a/test/unit/tool_shed/test_shed_index.py
+++ b/test/unit/tool_shed/test_shed_index.py
@@ -40,7 +40,7 @@ def community_file_structure(community_file_dir):
     return community(
         file_path=os.path.join(community_file_dir, "database", "community_files"),
         hgweb_config_dir=community_file_dir,
-        dburi="sqlite:///%s" % os.path.join(community_file_dir, "database", "community.sqlite"),
+        dburi="sqlite:///{}".format(os.path.join(community_file_dir, "database", "community.sqlite")),
     )
 
 
diff --git a/test/unit/tool_util/mulled/test_mulled_list.py b/test/unit/tool_util/mulled/test_mulled_list.py
index 07e71905a310..1eb3e5fa084a 100644
--- a/test/unit/tool_util/mulled/test_mulled_list.py
+++ b/test/unit/tool_util/mulled/test_mulled_list.py
@@ -25,7 +25,7 @@ def test_get_singularity_containers():
 def test_get_missing_containers():
     test_dir = tempfile.mkdtemp()
     try:
-        exclude_list = "%s/blocklist.txt" % test_dir
+        exclude_list = f"{test_dir}/blocklist.txt"
         with open(exclude_list, "w") as f:
             f.write("a\n\nb\nc\nd")
         containers = get_missing_containers(
@@ -39,7 +39,7 @@ def test_get_missing_containers():
 def test_get_missing_envs():
     test_dir = tempfile.mkdtemp()
     try:
-        exclude_list = "%s/blocklist.txt" % test_dir
+        exclude_list = f"{test_dir}/blocklist.txt"
         with open(exclude_list, "w") as f:
             f.write("a\n\nb\nc\nd")
         envs = get_missing_envs(
diff --git a/test/unit/tool_util/test_tool_deps.py b/test/unit/tool_util/test_tool_deps.py
index 89eb6f8e5ad5..13d84e3bb16c 100644
--- a/test/unit/tool_util/test_tool_deps.py
+++ b/test/unit/tool_util/test_tool_deps.py
@@ -322,10 +322,9 @@ def _setup_module_command(temp_directory, contents):
     module_script = os.path.join(temp_directory, "modulecmd")
     __write_script(
         module_script,
-        """#!/bin/sh
-cat %s/example_output 1>&2;
-"""
-        % temp_directory,
+        f"""#!/bin/sh
+cat {temp_directory}/example_output 1>&2;
+""",
     )
     with open(os.path.join(temp_directory, "example_output"), "w") as f:
         # Subset of module avail from MSI cluster.
@@ -483,10 +482,9 @@ def _setup_lmod_command(temp_directory, contents):
     lmod_script = os.path.join(temp_directory, "lmod")
     __write_script(
         lmod_script,
-        """#!/bin/sh
-cat %s/lmod_example_output 1>&2;
-"""
-        % temp_directory,
+        f"""#!/bin/sh
+cat {temp_directory}/lmod_example_output 1>&2;
+""",
     )
     with open(os.path.join(temp_directory, "lmod_example_output"), "w") as f:
         # Subset of a "lmod -t avail" command of the LMOD environment module system.
@@ -544,7 +542,7 @@ def test_shell_commands_built():
 
 
 def __assert_foo_exported(commands):
-    command = ["bash", "-c", '%s; echo "$FOO"' % "".join(commands)]
+    command = ["bash", "-c", '{}; echo "$FOO"'.format("".join(commands))]
     process = Popen(command, stdout=PIPE)
     output = process.communicate()[0].strip()
     assert output == b"bar", f"Command {command} exports FOO as {unicodify(output)}, not bar"
diff --git a/test/unit/util/test_lazy_process.py b/test/unit/util/test_lazy_process.py
index bc113a33df6e..a301b23ba5ab 100644
--- a/test/unit/util/test_lazy_process.py
+++ b/test/unit/util/test_lazy_process.py
@@ -11,7 +11,7 @@ def test_lazy_process():
     """Create process, ensure start_process starts it and shutdown kills it."""
     t = tempfile.NamedTemporaryFile()
     os.remove(t.name)
-    lazy_process = LazyProcess(["bash", "-c", "touch %s; sleep 100" % t.name])
+    lazy_process = LazyProcess(["bash", "-c", f"touch {t.name}; sleep 100"])
     assert not os.path.exists(t.name)
     lazy_process.start_process()
     while not os.path.exists(t.name):
diff --git a/test/unit/util/test_rule_utils.py b/test/unit/util/test_rule_utils.py
index 99641d0f0084..c14cefb10e9a 100644
--- a/test/unit/util/test_rule_utils.py
+++ b/test/unit/util/test_rule_utils.py
@@ -25,6 +25,6 @@ def test_rules():
                     assert final_source == expected_final_source, msg
 
         elif "error" in test_case:
-            assert rule_set.has_errors, "rule [%s] does not contain errors" % test_case
+            assert rule_set.has_errors, f"rule [{test_case}] does not contain errors"
         else:
-            raise Exception("Problem with test case definition [%s]." % test_case)
+            raise Exception(f"Problem with test case definition [{test_case}].")
diff --git a/test/unit/util/test_sqlite_utils.py b/test/unit/util/test_sqlite_utils.py
index 758733579c5b..ef234f9b81f3 100644
--- a/test/unit/util/test_sqlite_utils.py
+++ b/test/unit/util/test_sqlite_utils.py
@@ -52,8 +52,8 @@ def __assert_query_errors(connection, query, match):
 
 
 def __assert_allowed(query):
-    assert sqlite.is_read_only_query(query), "Query [%s] fails allowlist." % query
+    assert sqlite.is_read_only_query(query), f"Query [{query}] fails allowlist."
 
 
 def __assert_not_allowed(query):
-    assert not sqlite.is_read_only_query(query), "Query [%s] incorrectly fails allowlist." % query
+    assert not sqlite.is_read_only_query(query), f"Query [{query}] incorrectly fails allowlist."

From 6492f07b1731ee1f75a3bb5ef6fd546e96059634 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 29 Apr 2024 00:15:51 +0100
Subject: [PATCH 3/3] Fix for mypy 1.10.0

---
 lib/galaxy/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 4cb9358961c9..93ee001aed73 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -6409,7 +6409,7 @@ def attribute_columns(column_collection, attributes, nesting_level=None):
         for entity in return_entities:
             q = q.add_columns(entity)
             if entity == DatasetCollectionElement:
-                q = q.filter(entity.id == dce.c.id)  # type:ignore[arg-type]
+                q = q.filter(entity.id == dce.c.id)
 
         q = q.order_by(*order_by_columns)
         return q